Police were preparing to fly Batista from Sao Paulo, an AFP photographer at the airport said, a day after the tycoon turned himself in to the authorities.
Batista, the figure behind the rise of Brazil's JBS meatpacking giant, is accused of holding back evidence in explosive plea bargain testimony that threatens to bring down Temer.
Supreme Court Justice Edson Fachin said in a written ruling there was evidence that Batista and another executive "omitted... information that they were obliged to provide" as part of their agreement.
Fachin's ruling suspended the suspects' provisional release under the plea bargain and ordered them to be detained for five days.
The allegation against Batista upended the already dramatic corruption saga, which has left Temer fighting to remain in power and has damaged JBS. It also marks a radical change of fate for Batista himself.
The businessman and his brother Wesley admitted to prosecutors that they had bribed no less than 1,900 politicians.
It was the kind of large-scale graft network similar to those uncovered at other major Brazilian companies. But the bombshell allegation involved Temer.
To bolster the evidence, Batista met with Temer at his Brasilia residence in March and secretly recorded the president allegedly discussing payment of hush money to keep a former ally from testifying.
That recording and the Batistas' testimony then became key weapons in efforts by chief prosecutor Rodrigo Janot to put Temer behind bars. In return for their testimony, the Batista brothers appeared set to avoid prison.
A first criminal charge against Temer of bribe-taking lodged in June was rejected by Congress. However, Janot has been expected to file a second charge of obstruction of justice -- based partly on the Batista recording -- within days.
But the plea deal agreement, lambasted by Temer as a get-out-of-jail card for a "notorious bandit," is now under question.
And the confusion apparently started with what appears to have been a blunder by the tycoon's lawyers.
They were meant to send prosecutors more evidence under the plea deal but seemingly sent by error a recording in which Joesley Batista is said to be heard discussing with a former company director, Ricardo Saud, how he withheld important information from prosecutors.
The scandal has rocked Temer's already deeply unpopular government this year just as it was pushing reforms to try to drag Latin America's biggest economy out of its worst ever recession.
The future of the imbroglio is now more unclear than ever. Janot steps down on Sunday to be replaced by a new chief prosecutor - possibly leading to relief for the beleaguered Temer.