The move had not been widely anticipated after the former premier was allowed to leave prison to have his health checked for the first time since February.
Khan, 73, was transferred to a hospital during the intervening night of August 20 and 21 for medical examination, following a Supreme Court order this week, Information Minister Attaullah Tarar said in a post on X.
His supporters lined the streets of the capital Islamabad overnight, showering flowers on the vehicle widely believed to be carrying him to the hospital.
Aired live on Pakistani television, the images stood in stark contrast with how the country's broadcasters had covered Khan in recent years, tending to not even cite the highly popular cricketer-turned-politician's name until Thursday night.
Public perception that Khan was moved back to prison forcefully by authorities could spark new outrage among his supporters and potentially escalate tensions and street protests.
Khan's party, Pakistan Tehreek-e-Insaf, did not immediately comment on the claim that he was medically fit.
Senior party members had publicly interpreted the Supreme Court order as meaning that Khan would remain hospitalised at least for several weeks.
But Minister for Parliamentary Affairs Tariq Fazal Chaudhry told ARY News on Thursday that "if doctors decide that his treatment at the hospital is necessary, he will be admitted. If they opine that he can be treated in jail, he will be sent back."
In its order on Tuesday, the Supreme Court told authorities to transfer Khan to the Shifa International Hospital in Islamabad within two days and allow him access to a medical panel that includes his personal physician.
Tarar said Khan had been examined at the state-run Pakistan Institute of Medical Sciences hospital, rather than the private Shifa International Hospital, due to a "security situation created by PTI workers" along the planned route.
The PTI did not immediately comment.
It had told journalists in a statement overnight that Khan had arrived at Shifa International Hospital.
His sister Uzma Khan was present during the examination, Tarar said, and Khan was transferred back to Adiala jail in the garrison city of Rawalpindi at 5am.
Khan has been imprisoned since August 2023.
He says the cases against him are politically motivated, an accusation the government denies.
His lawyers say his health has deteriorated in prison and that he has lost significant vision in his right eye.
The government has said medical reports disclosed no condition requiring immediate treatment.
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