The 66-year-old Bolsonaro had been complaining publicly since last week about suffering from the hiccups following July 3 surgery on a dental implant.
Bolsonaro was first taken to a military hospital in the capital Brasilia but will now be transferred to Sao Paulo for more tests.
“He is in good spirits and feels well,” the presidency had said earlier in the day.
Bolsonaro was examined in Brasilia by Antonio Macedo, who has operated on the president several times since he was stabbed in the abdomen in 2018 while on the campaign trail.
If it is confirmed he needs an operation, it would be the seventh since he was stabbed by a former member of the Socialist and Freedom Party (PSOL), a group that broke away from the Workers’ Party (PT) of former president Luiz Inacio Lula da Silva, who is eyeing a run against Bolsonaro next year.
“Yet another challenge, a consequence of the assassination attempt carried out by a former member of PSOL, the left-wing arm of the PT, to prevent the victory of millions of Brazilians that wanted change in Brazil,” Bolsonaro wrote on Twitter.
Speaking to a local radio station last week, Bolsonaro had said: “This happened to me before, maybe due to the medicine I’m taking, I have hiccups 24 hours a day.”
On Tuesday night, a tired-looking Bolsonaro had complained to supporters outside his official residence in Brasilia about the problem.
“People, my voice has gone. If I start talking a lot, the hiccups return … they already have,” he said.
Bolosonaro also contracted Covid-19 last year although his symptoms were mild and he did not need hospital treatment.