However there were scenes of jubilation at his return, and Col Gaddafi then defied criticism from the UK and the US by meeting Megrahi on Libyan TV. The men were pictured talking and hugging.
The Scottish Government freed the 57-year-old prisoner, who is dying from cancer, on Thursday citing compassionate grounds.
Col Gaddafi praised the Scottish authorities, as well as "my friend" [Mr] Brown, the Queen and Prince Andrew for the role he said they played.
"This step is for the benefit of relations between Britain and Libya, and relations of personal friendship between me and them, and it will certainly be positively reflected in all fields of co-operation between the two countries," the Libyan leader said.
The UK Foreign Office has insisted the release of Megrahi - convicted of killing 270 people aboard a transatlantic airliner in 1988 - was a matter solely for the Scottish authorities.
Shadow foreign affairs minister, David Liddington, urged the government to be more open about its relationship with Tripoli.
"It is very important, I think, for the reputation of our institutions of justice that it is made clear beyond any doubt that this was not connected with some political trade," he said.
A former British ambassador to Libya, Sir Richard Dalton, called on the British government to be "more forthcoming in support of what the Scots have done".
"There are a number of outstanding questions and silence I don't think is serving the British interest well," he said. "In my view it was not naivety, nor was it opportunism."
'Slur on UK'
In an interview with a Libyan station, Col Gadaffi's son Saif al-Islam called Megrahi's release a "victory", and reportedly claimed that the issue had been raised repeatedly by Britain's former prime minister Tony Blair.
"In all commercial contracts, for oil and gas with Britain, (Megrahi) was always on the negotiating table," Mr Islam told Libya's Al Mutawassit channel.
Mr Blair visited Libya in May 2007, during which UK energy giant BP signed a $900m (£540m) exploration deal.
I never for a minute thought that it was just a question of compassionate release and the humanity and compassion of the Scots
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