Al Baghdadi al-Mahmoudi was extradited from Tunisia in June, making him the first senior Gaddafi official to be returned for trial under Libya's new leadership.
He went on trial in November charged with corruption and ordering mass rape during the 2011 conflict that toppled Gaddafi and is being held in a Tripoli prison.
On Tuesday, his Tunisian lawyer, Mabrouk Khorchi, said Mahmoudi was in critical condition and "risks dying" after being tortured in jail.
"Al-Mahmoudi is in good health, and is being treated humanely," Libya's present Prime Minister Ali Zeidan told a news conference.
"Our duty is to preserve his dignity ... The Mahmoudi trial is in the hands of the Libyan judicial system. The court will decide whether he is guilty or innocent."
The UN Support Mission in Libya (UNSMIL) said a team of its representatives had visited Mahmoudi at his detention centre on Thursday following Khorchi's statement.
"While most of the visit took place in the presence of the prison director, UNSMIL had the opportunity to talk to him privately for some time and asked whether he was mistreated. He unequivocally said he was not," UNSMIL said in a statement.
"Mahmoudi appeared in decent physical and psychological condition and his general demeanour was relaxed. He stated that he is being treated well, and although he suffers from various medical conditions, he has adequate access to medical care."
UNSMIL quoted Mahmoudi as saying he was being represented by a team consisting fully of Libyan lawyers and denied having any non-Libyan lawyers on his legal team.
"He expressed his wish to have more access to his lawyers and that they should be granted more access to the prosecution file against him. He said he has received some family visits, but not by his wife and children who are outside the country."
Mahmoudi served as Gaddafi's prime minister from 2006 until he fled to neighbouring Tunisia in August 2011 around the time rebel fighters took Tripoli. He could face life in jail or execution if convicted.
Human rights groups have questioned whether former officials can get a fair trial in a country where bitterness over Gaddafi's rule runs deep and the militias that helped unseat him have influence. But Libya's new leaders have said they are determined to show their state institutions are up to the job of conducting such trials.
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