"What is happening in France or in Portugal is not the fault of Mrs Merkel or of Germany," he is quoted as saying in weekly paper Welt am Sonntag.
"This crisis and the problems that go with it are not the result of German policies or the fault of the European Union. They are the result of excessive spending policies, of lack of competitiveness and irresponsible action by the financial markets," he said, according to the paper.
"The Eurogroup decisions are always taken unanimously. It's totally unfair to present these measures as though they were imposed by a single country or a single institution," Barroso was quoted as saying.
He added that Merkel "invests a lot of time and energy into the European project. I wish we could say the same for all the other heads of government."
Europe is becoming increasingly divided on the issue of austerity amid growing unpopularity with the public.
An attack last week by French Socialists on Merkel's drive for belt-tightening was the latest criticism of the German leader who is seen by many in Europe as the main driver of EU-imposed austerity.