He was responding to a question about the Times investigation from Francisco Guerreiro, a European lawmaker from Portugal.

Mr. Wojciechowski’s response, if short on specifics, signaled that top officials in Brussels are considering direct steps to combat corruption in the subsidy program. European officials had previously said that it was up to national leaders — including those who have manipulated and benefited from the subsidies — to institute reforms or crack down on abuses.

The Times tracked at least $49 million in subsidies to companies controlled by Prime Minister Andrej Babis of the Czech Republic, for example. And reporters mapped government farmland sales in Hungary that made the family and friends of the prime minister, Viktor Orban, eligible for millions of dollars in subsidies.

Despite such problems, any significant changes proposed by Mr. Wojciechowski are likely to be hotly contested. Some of the European lawmakers who write the subsidy policy also benefit personally from the program, a situation that is allowed by Europe’s weak and murky conflict-of-interest rules.

Cracking down will also be difficult because much of the abuse documented by The Times can be traced to the subsidy formula itself. The European Union pays farmers based on how much land they control, a system that encourages farmers to acquire more and more property.