According to the Brazilian magazine O Globo, military police blocked access to the Alvorada Palace in Brasilia after what it described as an attempted invasion.
A photo on the journal’s website showed a section of the gate knocked to the ground. It said bullet casings were also discovered.
Temer was reportedly not inside when the attack took place. The president has been highly unpopular in the country and there is a corruption probe against him on suspicion of bribery.
Earlier on Wednesday, Temer announced his decision to appoint Raquel Dodge as a new prosecutor general to replace Rodrigo Janot, who formally accused him of corruption on Monday. The lower house of parliament will now vote on whether Temer should be tried by the supreme court.