Security at the hospital has been stepped up
The heavily armed fighters - thought to be from Sudan or Yemen - are threatening to blow themselves up if anyone other than medical staff approaches them.
It is unclear how they managed to smuggle pistols and grenades into the hospital.
The men were part of a larger group of fighters who arrived at the hospital when the city was still under Taleban control.
They were left behind when the less seriously injured vanished after the Taleban surrendered the city.
"They are scared. They are ready to die if it is necessary. They have confidence in the nurses, but they don't want any unwanted guests", said Roland Nobs of the International Committee of the Red Cross, which funds the hospital.
The nine men were moved to a high security detention ward on Sunday which was previously used by the Taleban for political prisoners.
A civilian patient who was earlier being treated alongside the al-Qaeda men said they had been demanding that they should be freed and allowed to return to their home countries.
Head nurse Ghulam Mohammed Afghan said his staff were extremely worried about their safety while dealing with the fighters.
Surgeon Daud Farhad said: "I was shocked during examining an X-ray of one Arab patient when I saw a hand grenade fixed to his thigh." .
It is unclear what will happen to the al-Qaeda men under Kandahar's new governor Gul Agha Sherzai.
He has yet to establish a functioning administration and his forces have done nothing about the fighters so far.
Australian investigation
Meanwhile, the Australian government is investigating US media reports that an Australian citizen might be among the wounded at the Kandahar hospital.
Foreign Minister Alexander Downer said inquiries were under way, but with no diplomatic presence in Afghanistan it was difficult to confirm such reports.
He said his ministry had been contacted by the family of a 25-year old man believed to have gone to Afghanistan to fight with the Taleban.
He would be the third Westerner among Taleban and al-Qaeda fighters.
An American and an Australian captured earlier this months are now in US military custody.