The announcement comes after Yar'Adua returned to Nigeria early on Wednesday morning after more than three months abroad at a Saudi Arabian hospital.
Two aeroplanes arrived at the presidential wing of Abuja's Nnamdi Azikiwe international airport where one of them was met by an ambulance, the Reuters news agency, citing a witness, reported.
The ambulance later left under a heavy police escort. There was no immediate word on Yar'Adua's condition.
Following a power vacuum because of Yar'Adua's long absence from the country, Nigeria's parliament installed Jonathan as the acting head of state early this month.
Yvonne Ndege, Al Jazeera's West Africa correspondent, said that while Jonathan had established himself as a leader, constitutionally power still lay with Yar'Adua.
"There is potential, let's say, for Goodluck Jonathan to try to consolidate his position and become the substantive president of Nigeria," she said.
"But my sense is that that will have to come with the blessing of President Yar'Adua because if the constitution is followed to the letter of the law President Yar'Adua will be back in the seat of power."
Nigeria's constitution says the president must make a written declaration that he is on vacation or unable to carry out his duties before a transfer of power can take place.
Yar'Adua had not officially given his consent to the transfer of power, but parliament said it based its decision on an interview that he gave the BBC last month, saying that he would return to work once his doctors gave him the go-ahead.
Despite general government support, some critics have described the move to have Jonathan assume presidential powers as illegal.
Yar'Adua left Nigeria on November 23 to receive medical treatment at a clinic in Jeddah for pericarditis, an inflammation of the membrane surrounding the heart that can restrict normal beating.
He is also known to suffer from a chronic kidney condition and has long been criticised for not being able to work more than five or six hours a day.
Aside from the near constitutional crisis, Yar'Adua's long absence had prompted street protests by thousands across the country, demanding his resignation.
It also threatened to paralyse the government until parliament installed Jonathan as acting head of state on February 9.
A delegation of Nigerian ministers had travelled to Saudi Arabia on Monday to ascertain Yar'Adua's health, expecting to report back to a weekly cabinet meeting, but it appeared they had not managed to see him.
Instead they were told that he was on his way back to Abuja.
Nii Akuetteh, the former executive director of Africa Action, said that could have been a deliberate move to avoid further conflict.
|There was no word on the health of Yar'Adua, seen here in a picture from last July [EPA]
"My impression is now that the delegation that went to Jeddah [was] a small portion of the cabinet," he told Al Jazeera.
"Now the entire cabinet, if they want to assess the president's health, will have him there to do that instead of depending on a few people who went to Jeddah and can come back with conflicting reports."
The Nigerian presidency reflects a regional balancing act between the Muslim north and the Christian south, with the role traditionally switching between the two sides with every election.
Yar'Adua is from the Muslim north and Jonathan from the Christian south.
While many activists in the south would be pleased to see a southerner in the presidency, others from the north would like their candidate to serve a full term.
"A lot of this was precipitated by people from the south - activists - who actually went to court to say that he [Yar'Adua] has been away for too long," Akuetteh said.