The visit ended sooner than his supporters expected, with his party saying the process violated a top court directive.
The former premier's Pakistan Tehreek-e-Insaf (PTI) party said the Supreme Court order earlier this week meant Khan should remain under medical supervision until at least mid-September.
Khan was examined at the state-run Pakistan Institute of Medical Sciences hospital, rather than the private Shifa International Hospital recommended by the court, due to a "security situation created by PTI workers" along the planned route, Information Minister Attaullah Tarar said on X, a move Khan's party termed an "open violation" of the court order.
"Bring forward the full reports, comply with the order. Health is not propaganda, it is a fundamental human right," PTI spokesperson Sheikh Waqas Akram said in a post on X on Friday.
Public perception that the highly popular Khan was moved back to prison forcefully by authorities could spark new outrage among his supporters and potentially escalate tensions and street protests.
The cricketer-turned-politician's 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 ousted leader's name until Thursday night.
Senior PTI members had expected Khan to remain hospitalised at least for several weeks after he was allowed to leave prison to have his health checked for the first time since February.
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.
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.
