Geddel Vieira Lima, a former cabinet minister, had been in charge of Mr Temer's relations with Congress.
Prosecutors say Mr Vieira Lima tried to block investigations into state bank Caixa Economica Federal. There was no immediate comment from Mr Vieira Lima.
Mr Temer is fighting a corruption crisis that has shaken his government.
Last week Brazil's prosecutor general also charged Mr Temer and an aide with corruption.
Mr Temer has denied the accusations against him and says he has support in the Congress which will begin to discuss the charges this week.
If two-thirds of the lower house vote in favour, Mr Temer will be suspended from office for 180 days and tried in the Supreme Court.
The president's latest political crisis began in May when a business tycoon secretly recorded a conversation with the president in an unofficial late-night meeting which he revealed in a plea bargain deal with prosecutors.
During the conversation, Mr Temer appeared to endorse the tycoon obstructing the investigation and bribing politicians.
Mr Temer has said the footage is authentic, taken from a meeting in March, but he has strongly denied wrongdoing.
His administration has been bogged down with a string of corruption scandals since he took over from former president Dilma Rousseff in a controversial impeachment process.
Brazilian police have arrested a close ally of President Michel Temer as part of a corruption investigation into a government-controlled bank.