"Assurances had been given by the Libyan government that any return would be dealt with in a low-key and sensitive fashion. I regret very much that those assurances were not adhered to," said.
The Scottish government's emergency session was held as it faced unrelenting criticism from the US government, the families of some bombing victims and politicians within the UK.
Al-Megrahi, 57, who is dying from prostate cancer, was released from prison in Scotland last Friday.
He had been sentenced to life in prison in 2001 for planting a bomb on Pan Am Flight 103, which killed 270 people when it exploded over the Scottish town of Lockerbie on December 21, 1988.
MacAskill told Scottish ministers he would co-operate with any inquiry into al-Megrahi's release.
He also deflected concern from ministers worried about the decision's impact on Scotland's international standing, after it provoked an online campaign to boycott Scotland and Scottish goods.
The British government has also come under pressure to explain its role in al-Megrahi's release, denying claims it was linked to trade deals.
Saif al-Islam, son of Muammar Gaddafi, Libya's leader, said earlier that his release had often been raised in talks with Britain over oil and gas.
"In all commercial contracts, for oil and gas with Britain, [al-Megrahi] was always on the negotiating table," he told Libyan television on the weekend.
But Peter Mandelson, Britain's business secretary and Prime Minister Gordon Brown's de facto deputy, categorically denied that a deal had been struck with Libya to allow al-Megrahi to walk free.
Al-Megrahi has steadily maintained his innocence, but last week dropped his appeal so that he could be released on compassionate grounds.