Folha newspaper published what it said were excerpts of secretly taped conversations in March between Planning Minister Romero Juca and Sergio Machado, an ex-president of Transpetro oil company, both of whom have been caught up in the corruption probe.
In the conversations, Juca allegedly calls for a "national pact" to stop the probe, known as Operation Car Wash, in which dozens of top ranking politicians and business executives have been charged or already convicted for participation in a giant bribery and embezzlement scheme centered on state oil company Petrobras.
In comments immediately taken up by Rousseff supporters as evidence for her claim that the impeachment process is a coup in disguise, Juca says: "I am talking to the generals, the military commanders. They are fine with this, they said they will guarantee it."
According to the transcripts, he also says that he has been clearing his plans with justices on the Supreme Court, which oversees impeachment proceedings.
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But Juca -- a key figure in the new cabinet set up by acting president Michel Temer after the suspension May 12 of Rousseff -- denied that his comments referred to halting Operation Car Wash.
In a hastily called press conference, Juca said he backed the Car Wash probe and said that Folha had taken "isolated phrases" out of context.
"I consider Car Wash as bringing positive change to Brazilian politics," he said.
"There is nothing wrong in being investigated -- there's something wrong in being convicted," he said. "I have never done anything that could complicate an investigation."
The report meant fresh scandal for Temer, who took power 10 days ago after the Senate voted to suspend Rousseff for six months pending her impeachment trial on charges of breaking government accounting rules. Temer, a vice president who had already broken ranks and turned rival, automatically took over.