The UK Government has published details of a deal struck with Libya on prisoner exchange, which it insists does not cover the Lockerbie bomber's case.
Scotland's First Minister Alex Salmond had voiced concern at Holyrood that Abdelbaset Ali Mohmed al-Megrahi could be transferred back to a jail in Libya.
A spokesman for Prime Minister Tony Blair said no deal had been signed over the future of al-Megrahi.
The Libyan is serving life for killing 270 people in the 1988 Pan Am bombing.
He was convicted in 2001 of blowing up Pan Am flight 103 over the Scottish town of Lockerbie.
He was tried under Scottish law at a specially convened court at Camp Zeist, in the Netherlands, and is currently held in Gateside Prison in Greenock, near Glasgow.
The memorandum of understanding with Libya was signed last week by Mr Blair during a trip to the country. It was created on 29 May.
It states that the two sides will shortly "commence negotiations" on prisoner transfer, extradition and mutual assistance in criminal law, with a final deal signed within 12 months.
It will be based on a "model agreement" that, according to the document, has already been hammered out.
Mr Salmond had demanded clarification from the UK Government about al-Megrahi's case and made an emergency statement at Holyrood on Thursday.
He said that "at no stage" was the Scottish government made aware of the memorandum, despite the deal being struck on 29 May.
Addressing MSPs, he said: "I have today written to the prime minister expressing my concern that it was felt appropriate for the UK government to sign such a memorandum on matters clearly devolved to Scotland, without any opportunity for this government and indeed this parliament to contribute."
The first minister reminded politicians that al-Megrahi's case was being reviewed by the Scottish Criminal Cases Review Commission, which could send his case back to appeal judges in Edinburgh.
Prosecutors have called for a longer sentence, while al-Megrahi's team have been seeking a reduction.
Scotland's top law officer, the Lord Advocate Eilish Angiolini, supported the decision to write to Mr Blair, Mr Salmond said.
The first minister made an emergency statement to Holyrood
He added that while the Scottish Executive supported the UK Government's desire for better relations with Libya, the lack of consultation with Holyrood over the memorandum was "clearly unacceptable".
"This government is determined that decisions on any individual case will continue to be made following the due process of Scots law," the first minister said.
A Downing Street statement said: "There is a legal process currently under way in Scotland reviewing this case which is not expected to conclude until later this summer.
"Given that, it is totally wrong to suggest the we have reached any agreement with the Libyan Government in this case.
"The memorandum of understanding agreed with the Libyan Government last week does not cover this case."
A spokesman for the prime minister said a deal covering Libyan prisoner exchange was reached between Mr Blair and the Libyan leader Colonel Gaddafi.
Lack of consultation
When asked if after the legal review al-Megrahi could be returned to serve his sentence in Libya, the spokesman would not be drawn.
Opposition politicians in Scotland condemned the lack of consultation with the Scottish government.
Labour leader Jack McConnell said: "As former first minister I would have expected and demanded no less than prior consultation on such a memorandum.
"Scottish ministers, as far as I understand the letter of the law, have an absolute veto over prison transfers. I want to know if this memorandum contradicts that in any way."
However, he went on to criticise Mr Salmond for not telling MSPs sooner.
Mr Salmond told him he became aware of the memorandum on Friday, discussed it at the Scottish Cabinet meeting on Tuesday and then consulted the lord advocate on Wednesday.
Scottish Tory leader Annabel Goldie said: "Tony Blair has quite simply ridden roughshod over devolution and treated with contempt Scotland's distinct and independent legal system."
Liberal Democrat leader Sir Menzies Campbell said: "The government's ineptitude in handling this matter has given Mr Salmond precisely what he wanted.
"Westminster and the Labour government have given the impression of disdain for the Scottish authorities.
"The issue is not large in itself but it has played right in Mr Salmond's hands."
Former Labour MP Tam Dalyell, who has believed throughout in al-Megrahi's innocence, said: "The prime minister may think he can draw a line under all this.
"Surprisingly I am sympathetic to Mr Salmond. The only way that Megrahi can prove his innocence is through the Scottish legal system."
Dr Jim Swire, whose daughter Flora was killed in the bombing and who speaks for other British victims, said Scotland had been insulted by the British-Libyan agreement.
Referring to the document, he said: "Incredibly it seems that we are being asked to believe that this concerns other Libyan nationals, but not Megrahi.
"No mention of any discussion was given to us, the Lockerbie relatives.
"Mr Salmond should indeed remain indignant: Scotland has been insulted."