The Staff Union of the EPO (SUEPO) sent a letter to the President of the European Parliament, Jerzy Buzek, warning of risks for the European Parliament to be "circumvented" as a legislator when the EU will accede to the European Patent Convention (EPC). The European Patent Organisation is everything except a model of democracy: national patent offices are in power, there is no parliament involved in the decision making process, and diplomatic conferences are held behind closed doors.
Here is the letter in plain text, with some parts I put in bold:
INTERNATIONALE GEWERKSCHAFT IM EUROPÄISCHEN PATENTAMT
STAFF UNION OF THE EUROPEAN PATENT OFFICE (SUEPO)
UNION SYNDICALE DE L'OFFICE EUROPEEN DES BREVETS (USOEB)
Zentraler Vorstand - Central Executive Committee - Bureau central
10 May 2010
su10050cl - 3.2/0.4.2
For the attention of the Members of the European Parliament involved in intellectual property issues
EU Patent legislation
Accession of the European Union to the European Patent Convention
Dear Madam, dear Sir,
The European Parliament is currently preparing its position with regard to the EU Patent system and EU patent legislation. SUEPO, the Union of European Patent Office employees , is concerned about the shape of the future institutional cooperation between the EU and the EPO and wish to draw your attention to this subject.
Commission and Council consider the European Patent Office, an intergovernmental body established outside the EU institutions, as the right entity to take on the important public authority task of processing and granting EU patent applications. SUEPO welcomes the trust granted to the EPO. SUEPO shares the Commission's and the Council's opinion that Europe's existing, complex patent system urgently needs upgrading in order to meet the needs of the EU's "Lisbon Agenda": the European patent system currently lacks a single patent title and single patent jurisdiction . Due to the split legislation there is also a lack of efficient coordination between EU patent policy and other relevant EU policies in the field of intellectual property policy (plant varieties, trade marks, etc…), competition, internal market issues, regional and SME policies.
However, the public percieves legislation under the existing intergovernmental European patent system to be intransparent. Further, the strong presence of chief executive officers of national patent offices in the governing body of the EPO, the EPO Administrative Council, results in an unhealthy competition between the European Patent Office and the national patent offices. It also hinders the harmonization of quality and renders more difficult an efficient distribution of tasks between the EPO and the national patent offices which is in the interest of the users of the system .
SUEPO is concerned about the future institutional link between the EU institutions and the EPO. In our view, gearing the EPO to the EU legislator can only be achieved effectively through the accession of the EU to the EPO: i.e. when the EU becomes a signatory of the EPC. The institutional concept allowing an efficient and legally sound gearing of the two organisations is available . This concept would permit the EU to rely on the EPO to grant EU patents that are examined under legislation truly legitimated by EU legislative processes. In contrast, any contractual relationship between the EU and the EPO, should such an option be considered, would raise a number of serious legal undertainties.
1. It is particularly worrying that currently the EPO bodies, including legislative  and judicial  bodies, feel that they are not formally bound by EU legislation.
2. If a simple contractual relationship between EU and EPO is opted for, the procedures that allow the European Parliament to be involved in the legislative process (Ar. 218 EU Treaty) can be circumvented. Procedures allowing the European Parliament to hold the Commission accountable have no effect on a legislator - like the EPO - that is institutionally located outside the EU Institutions. The draft EU Patent Regulation , which is based on Art.118 of the EU Treaty, incorporates the EPC which may change in substance according to the wishes of the 37 EPO member states. Under a contractual relationship, an external legislator would be allowed to substitute into legislation under Art.118 EU Treaty. This would entail a loss of procedural rights of the European Parliament and introdude a structural inconsistency in the EU legislative process.
3. EU patent applications and third parties alike could challenge the validity of the EPO decisions based on international constitutional law, inspired by the appeal filed by a German businessman before the German Constitutional Court  (unconstitutionality of the European arrest warrant). Indeed, it is doubtful whether the European Patent Convention (EPC) provides for sufficient legal basis for the EPO to conclude far reaching agreements between the EU Member States and the EU (neither Art.40 EPC, nor Art.149 EPC).
4. Following the "Lisbon" judgement of the German Constitutional Court , the validity of the envisaged EU Patent Regulation itself could be challenged based on the failure to meet constitutionality standards equivalent to German standards, since an important element for the creation of the EU Patent, the EPC, would stay outside of constitutionally safe legislation.
5. Litigation brought before the ECJ (Court of Justice of the European Union) by patent applicants of third parties  may entaila a challenge of the validity of the EU Regulation itself, for instance because of a lack on involvement of the EU Parliament.
6. The danger described for the EU Patent Regulation may also apply to the decisions of the European and Community Patent Court, since the agreement on this Court (Art. 14) foresees the applicability of the EPC also for the validity assessment of EU Patents.
It would be highly problematic that individual patent applicants, patent owners or third parties be put in a position of challenging the validity of the whole European legislative construction. The risk taken in opting for a contractual relation between the EPO and the EU would be entirely disproportionate.
In the light of the considerations above we urge you to give the considered accession of the EU to the EPO under Art.218 EU Treaty the highest attention. Should you have doubts on the relevance of the questions raised by SUEPO, we suggest that an opinion be requested from the European Parliament's Legal Service.
Edward Daintith Chairman SUEPO Central Executive Committee
Desmond Radford Chairman SUEPO The Hague
Dorothée Heller Chairwoman SUEPO Munich
Carmen Schuhmann Chairwoman SUEPO Vienna
Peter Kempen Chairman SUEPO Berlin
Copy: Mr J. Buzek, President of the European Parliament Mr M.Barnier, Commissioner, DG MARKT
 SUEPO is an affiliate of Union Syndicale Fédérale (USF), European Public Services Unions (EPSU), European Trade Unions Confederation (ETUC)
 Harhoff, Economic Cost-Benefit Analysis of a Unified and Integrated European Patent Litigation System, Final Report, Study commissioned by DG MARKT of the European Commission, Tender No. MARKT/2008/06/D, 31 December 2008, as revised on 9 February 2009, p. 40; see also Van Pottelsberghe in http://www.bruegel.org/uploads/tx_btbbreugel/pb_201002_300310-2.pdf
 Van Pottelsberghe, Danguy, Economic Cost-Benefits Analysis of the Community Patent, Study commissioned by DG MARKT of the European Commission, 7th April 2009, http://ec.europa.eu/internal_market/indprop/docs/patent/studies/litigation_system_en.pdf
 Council document 14551/03, 13th November 2003
 EPO Official Journal 8-9/1999, p.573, paragraphs 2-3: "2. Directive 98/44/EC of the European Parliament and of the Council of 6th July 1998 (hereafter the Directive) on the legal protection of biotechnological inventions entered into force on the 30 July 1998. EU member states are required to implement it in national law by 30 July 2000. 3. The European Patent Organisation itself is not subject to this formal requirement."
 See decision of the Enlarged Board of Appeal of the EPO G 1/06, point 6: "The Boards of Appeal apply the provision [the Directive] because it is law under a specific Rule of the Implementing Regulations to the EPC, and not because the Directive is a source of law to be applied directly."
 Council document 8588/09, 7th April 2009
 Bundesverfassungsgericht, judgment of the18th July 2005, "2 BvR 2236/04"
 Bundesverfassungsgericht, "Lisbon Treaty judgement", “2 BvE 2/08, 2 BvE 5/08, 2 BvR 1010/08, 2 BvR 1022/08, 2 BvR 1259/08, 2 BvR 182/09”
 Art.48 of the Draft European and Community Patent Court agreement, Council document 7928/09, 23rd March 2009
Here is the full letter in images, also a copy in PDF:
There is a pending report on "Community innovation policy in a changing world" led by Hermann Winkler (PPE) in the European Parliament (that will come to plenary for a vote in June), and some amendments at the committee stage were already quite critical of the future role that will be played by the European Parliament patent law:
FFII comments on the Winkler report: "European Parliament not a legislator of second class"
April 27 2010
Dear Member of the ITRE Committee,
I am writing to you regarding the pending Winkler report on reviewing
Community innovation policy in a changing world (2009/2227(INI)) . For me
it seems an important initiative to address the institutional deficits that
stifled the ambitious Lisbon innovation goals.
I am very delighted about amendment 103 and ask you to lend your support to
"22b. Warns against the proposal to set up an International Patent Court
within the United Patent Litigation System draft Treaty, and points to the
fact that such a Court would not be counterbalanced by any legislative
assembly, let alone the European Parliament;"
In 2003 the FFII coined the slogan "Power to the Parliament". It is known
that the European Parliament rejected the controversial software patent
directive in 2005 . Less then 6 months after the rejection of the bill,
the patent lobby asked to get a specialised court in place.
The Parliament had also passed a resolution in 2006  asking for
assessments of "patent quality, governance of the patent system, judicial
independence and litigation costs".
The pending UPLS international treaty will create a patent court outside
of the EU system, outside of the European Parliament, and outside of the
European Court of Justice .
Please have your say on the attempts to make the European Parliament
defunct as a legislator in patent matters, and endorse amendment 103.
HENRION Benjamin <bhenrion at ffii.org>
President of FFII.org
I have to note that the position of SUEPO is not quite consistent with what they have pushed in their past positions papers (the source is their submission to the Consultation on the Green Paper in 1997, I still have to find a copy of that, but I quoted it in one of my presentation "EU vs EPO" at the EPO conference in Ljubljana in 2008):
"As proposed by the founding fathers of the European patent system, the Staff Union of the EPO proposes the return of the entire European patent system to the framework of Community law […] The EPO should be integrated into the Community Institutions, which alone are capable of exercising a political control taking into account public interest at European level"
If you still have a copy of this submission by the SUEPO, I would be interested to have one. It should be available on request at the European Commission. Furthermore, I know that some examiners submitted a petition to the European Parliament on this subject.
Now with the proposed UPLS plans, it seems that the European Union will be absorbed by the European Patent Organisation, not the other way around. European Parliament won't have a direct control of the european patent office.