The presidential palace quickly responded, saying Temer "never deployed (Abin) to investigate the life of Supreme Court Minister Edson Fachin, as was reported".
"There are serious proven facts but not enough to annul the mandate", the judge added.
The news comes after reports that Brazil's Electoral Court resume trial into the allegations that the impeached President Dilma Rousseff and sitting President Michel Temer, who had been vice president then, received illegal funding in the presidential campaign of 2014.
Temer himself is now under investigation for bribe taking and obstruction of justice related to the array of interlocking "Car Wash" corruption scandals.
"While Temer is hard for many people to digest, he will likely remain in office", said Alexandre Barros, a political risk consultant with the Brasilia-based firm Early Warning.
The case against Temer was bolstered after dozens of current and former executives at the construction company Odebrecht provided details about millions of dollars in bribes and illegal campaign donations as part of a plea-bargain.
Temer denies all the charges against him, but now that the election controversy has been put aside he is believed to be gearing up for an intensified fight with prosecutors over the corruption allegations. They also clashed over the strength of the original evidence and whether punishments should be doled out when illegal campaign finance was widespread.
May 'sorry' for election result which cost Tory MPs their seats
So we're looking forward to seeing whoever May picks to send to Brussels on her behalf to get the "best" deal available on Brexit. Adding more time to the two-year schedule would require unanimity amongst the EU-27, which would be legally complicated.
If they had been convicted, Mr Temer could have been suspended from the presidency while Ms Rousseff would have lost her political rights.
His already very low popularity has plunged further amid the corruptions allegations.
While Temer had vowed to appeal a conviction, it would have weakened his hand in a climate of several corruption scandals and a public furious about it. "I don't think anybody is in the mood to decide something unexpected at this point". There are near weekly protests calling for Temer's ouster, frequent shouting matches in Congress, and a simmering debate in the media over whether Temer will manage to finish out his term. However, the court justice overseeing the Car Wash investigation ordered Rocha Loures removed from his post last month while a corruption investigation case against him runs its course. As the tension in the chamber rose, the court's president called a brief break.
Brazil finally emerged out of recession in the first quarter of this year, after two years of negative growth, and Mr Temer said he was the only one capable of bringing the stability needed for full economic recovery.
"The days ahead will be very hard for Temer".
The acquittal will help Temer retain key coalition allies who will support his fiscal reform agenda approval in Congress.
Ironically, Temer's strongest claim to stay in power is the argument that he can deliver major reforms to labor laws and the country's pension system.
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