BRUSSELS — European Union lawmakers on Tuesday strongly criticized corruption and self-dealing in the bloc’s $65-billion-a-year farm subsidy program but were sharply divided over how or whether to reform a system that has become a third rail of European politics.

At a time of festering anti-European sentiment, the debate over one of the world’s largest subsidy programs highlighted a fissure that cuts far deeper than a simple dispute over farm policy. It raised the question of how to combat political corruption without infringing on the independence of the bloc’s 28 nations — and further emboldening its far-right populist critics.

Tuesday’s debate happened during a European Parliament budget oversight hearing, which was prompted, in part, by a New York Times investigation into the farm subsidy program, known as the Common Agricultural Policy or C.A.P. In November, the Times revealed how subsidies help underwrite oligarchs, enrich politicians and encourage land-grabbing and Mafia-style tactics.

“The recent New York Times report on the abuse of C.A.P. subsidies is damning and undermines trust in government,” said Mick Wallace, a European lawmaker from Ireland.