Mr Bolsonaro’s beach vacation, which started on December 27, triggered controversy in recession-hit Brazil.
With the northeastern state of Bahia battered by deadly floods, the president ignored calls to interrupt his holiday, instead posting videos of himself soaking up the sun and jet skiing through crowds of cheering supporters.
Doctor Antonio Luiz Macedo, the surgeon who heads the medical team and has operated on Mr Bolsonaro in the past, told news site UOL the president would undergo a battery of tests.
In July, Mr Bolsonaro spent four days receiving treatment for an intestinal obstruction.
Since the knife attack, he has undergone abdominal surgery at least four times.
He regularly becomes tearful when speaking about his stabbing in September 2018, perpetrated by a lone assailant who was found to be psychologically unfit for trial.
Doctors said Mr Bolsonaro lost 40 per cent of his blood in the attack, which nearly killed him.
But he survived and went on to win the presidency that October, fueling supporters’ die-hard faith in the man they call “Mito” – “The Myth.”
Mr Bolsonaro’s aura of invincibility has faded since then, however.
His approval rating is at an all-time low as he prepares to seek re-election this October.
Mr Bolsonaro trails far behind his likely top opponent, leftist ex-president Luiz Inacio Lula da Silva (2003-2010), whom recent polls indicate could win the election in the first round.