First Minister Alex Salmond has written a second letter of protest to Prime Minister Tony Blair in the row over the fate of the Lockerbie bomber.
Tony Blair met Colonel Gaddafi in Libya last month
He had complained that the Scottish government was not consulted before a memorandum of understanding on prisoner transfer was signed with Libya.
Mr Salmond said he was disappointed with the formal reply he received from the Lord Chancellor, Lord Falconer.
That letter says Scottish ministers would have the final say on transfers.
Lord Falconer has attempted to reassure Mr Salmond that nothing Tony Blair signed with Colonel Gaddafi committed anyone to the transfer of any particular Libyan prisoner, let alone Abdelbaset Ali Mohmed al-Megrahi.
He said it was "quite proper" for the UK Government to negotiate foreign policy with other countries and said it would consult with the devolved
administrations before entering into "any international agreement that would bind those administrations in a matter devolved to them".
And he added: "The UK Government recognises that the decision to transfer any prisoner held in a Scottish prison is a matter for the Scottish ministers."
However, the first minister said he was disappointed with the letter.
He has written a two-page reply to the prime minister, not Lord Falconer.
Mr Salmond says in the letter that the talks in Libya were in breach of one of the devolution concordats which states Scottish ministers should be consulted in advance over foreign treaties that affect Scotland.
The first minister asks whether the al-Megrahi case was discussed during the talks and whether the Libyan would be specifically excluded from the final agreement.
Mr Salmond concludes his letter by saying: "I regret that you did not choose to reply personally to my previous letter.
"I do hope that you will feel able to address the two specific points raised above personally."
Abdelbaset Ali Mohmed al-Megrahi is serving a life sentence
The fact that Mr Blair did not reply to Mr Salmond's first letter personally is being seen by the first minister as another snub.
He is still waiting for a call or letter of congratulation on being elected first minister.
Scottish Conservative leader Annabel Goldie MSP accused the prime minister of "ineptitude and insensitivity".
"He is putting his own ego before the greater interest of the stability of the Union, and playing right into the hands of the Scottish Nationalist first minister," she said.
"The sooner Tony Blair's successor realises this, takes charge of this situation and starts responding appropriately and sensibly, the better.
"Equally, we must know the details of any discussion or correspondence entered into between the Scottish Executive and the Westminster Government, prior to last week's statement in the Scottish Parliament."
Al-Megrahi is currently being held in Gateside Prison, Greenock, near Glasgow, as he serves life for killing 270 people in the 1988 Pan Am bombing.