Former speakers Eduardo Cunha and Henrique Eduardo Alves, as well as Temer's current chief of staff Eliseu Padilha and Cabinet Minister Wellington Moreira Franco, participated in Temer's scheme, Batista said in the interview.
"Temer is the leader of a lower house criminal organization," Epoca quoted Batista as saying. "Those who are not under arrest are in the government. They're very dangerous."
Temer's media office declined to comment. Press representatives for Batista and his family's investment holding company, J&F Investimentos SA, were not immediately available for comment.
Efforts to reach the lawyers of Cunha, Alves, Moreira Franco and Padilha were unsuccessful.
The comments took Batista's accusations against Temer a bit further since the billionaire entrepreneur told prosecutors that Temer worked to obstruct an ongoing corruption investigation as president.
Rousseff was impeached last year on accusation she oversaw the doctoring of budget accounts.
J&F agreed to pay a record-setting 10.3 billion-real ($3.1 billion) leniency fine, after Joesley Batista and his brother Wesley admitted to bribing almost 1,900 politicians in recent years. J&F-controlled JBS SA, the world's premier meatpacker, is being investigated for alleged insider trading ahead of the announcement of the Batista family's leniency deal.
Batista denied having ordered insider trades at JBS, according to the Epoca interview, adding that he believed they were all made in line with the law.
He said J&F will sell "as many assets as necessary" to quash concerns about the group's solvency. J&F diversified from meatpacking in recent years, expanding into fashion, home cleaning, banking and pulpmaking with the help of state loans, prosecutors said.