Speaking at a conference on the Lisbon Treaty, which entered into force on 1 December 2009, Barroso said member countries had opted for intergovernmental talks instead of using the slower 'Community method', which involves the EU institutions.
Last May, eurozone countries moved alone in their attempt to rescue the EU currency and rejected the European Commission's proposals, Barroso said. France and Germany steered the response to the Greek sovereign debt crisis by drafting a joint letter and then seeking support for their proposals.
The second occasion, Barroso said, came at the last EU summit on 4 February, when German Chancellor Angela Merkel and French President Nicolas Sarkozy presented their Pact for Competitiveness.
Barroso supported the Franco-German pact, but added that the best guarantee for "preserving the coherence" of the initiative was the Community method, involving the European Commission as the guardian of the EU Treaties. "This is the best guarantee against possible divisions within our Union," he said, speaking in French.
The intergovernmental "temptation" is not something new, as member countries are "under different kinds of pressure" to move forward without consulting their European partners, Barroso said. But he added that as Commission president, it is his duty to insist on a more inclusive method involving all EU institutions. He added that he had done so during last Friday's summit.
Guy Verhofstadt, leader of the liberal ALDE group in the European Parliament and one of Brussels' most vocal promoters of federalism, encouraged the Commission president to resist the drift towards intergovernmentalism.
In a letter which appears to mark a rapprochement between the two men, Verhofstadt called on Barroso to present a bold and comprehensive package of proposals to boost competitiveness and governance ahead of the March European Council, rather than leaving an empty space for Germany and France to fill.
In an interview with Belgian daily Le Soir, EU Trade Commissioner Karel de Gucht said the new European Commission had become much more political and much more "powerful" than any national government. In a national government, you have to agree between coalition members, while the Commission can decide by majority vote, De Gucht argued.
"The Commission is a system that doesn't get blocked," he said.
