Temer's office acknowledged he had met in March with the businessman Joesley Batista, chairman of meat giant JBS SA, but denied any part in alleged efforts to keep jailed former House Speaker Eduardo Cunha from testifying.
O Globo's report threatens to pull Temer into a corruption scandal that has already entangled several of his closest allies and advisers.
Leading lawmakers and a third of his cabinet have already been caught up in a probe of systematic bribery, in return for political favors and contracts with state-run enterprises. But news the president himself may have been party to a cover-up shook the scandal-weary nation.
Investors dumped Brazilian assets in foreign markets after the news broke, as the prospect of Temer becoming enmeshed in a fresh political crisis clouded the prospects for his unpopular reform agenda, considered key to ending a deep recession.
Scattered protests sprang up in front of the presidential palace and along Sao Paulo's main avenue, as opposition lawmakers and even a high-profile ally called for him to step down.
"Given the gravity of the situation, and the responsibility to keep Brazil from plunging into the imponderable, the only option is for President Michel Temer to resign," said Senator Ronaldo Caiado, leader of the government-allied Democratas party in the Senate.
Temer's office said the president "did not participate in or authorize any activity with the aim of avoiding a plea bargain or collaboration" by Cunha, adding that he supported a full investigation of the allegations.