France and Germany, for instance, bypassed the EU in steering a response to the Greek crisis by drafting a joint letter and then seeking support for their proposals, European Commission President Jose Manuel Barroso said.
And eurozone countries moved alone in their attempt to rescue the euro, rejecting EC proposals, he said.
While he did not condemn these efforts, he said they could lead to patchwork efforts that could possibly be divisive, compared with the often-slower "community method" involving EU institutions, which he said was best for "preserving the coherence" of EU country plans.
"This is the best guarantee against possible divisions within our union," Barroso told reporters in French.
Germany and France had no immediate comment.
German Chancellor Angela Merkel proposed Friday working with the 27-member union to save the euro, with a plan that the EC would verify.
Barroso critics said the EC -- the EU's executive body, responsible for proposing legislation, implementing decisions, upholding union treaties and the union's general day-to-day operations -- is slow to come forward with meaningful initiatives, the EUobserver newspaper said.
"The lack of such proposals can only lead to certain member states believing they are better off going it alone," Belgium's Guy Verhofstadt, the leader of the European Parliament's Liberal group, wrote to Barroso.
Barroso is a former Portuguese prime minister, whose own country is trying to work through its sovereign-debt crisis without EU assistance.
Notable deaths of 2014 [PHOTOS]
Ebola health workers killed in Guinea