James Robertson, acclaimed by First Minister Alex Salmond and many others as Scotland's finest living writer, says he is in broad terms in favour of Scottish independence.
But he adds: "I wouldn't want to go into a referendum with people saying our justice system is not in good health and able to point to Lockerbie to support that view."
He said that because of the uncertainty surrounding the conviction of Abdelbaset Ali Mohmed al Megrahi, "there is an enormous stain on the Scottish justice system and we cannot move forward without erasing it".
Mr Robertson, best known for And The Land Lay Still and The Testament of Gideon Mack, has taken a profound interest in Lockerbie, and it has influenced his latest novel, The Professor of Truth, to be published by Penguin in May 2013.
Last year he delivered a compelling Saltire Society lecture at the Edinburgh International Book Festival, spelling out why he believed Megrahi had suffered a miscarriage of justice.
He also wrote to Mr Salmond to express support for the calls of the UK relatives for a full and independent inquiry, and was disappointed to receive the standard response – that the Scottish Government had no reason to doubt the safety of Megrahi's conviction.
Mr Robertson said: "If the Scottish Criminal Cases Review Commission saw clear grounds for a second appeal, it's hard for the Government to continue to justify that position.
"We need a full and independent inquiry to resolve it, very obviously for the sakes of the relatives, but also to underline Scotland's integrity if we are to move towards independence."
Megrahi was found guilty in 2001 of blowing up Pan Am Flight 103 over Lockerbie in 1988, an atrocity that claimed the lives of 270 people.
He was released from prison on compassionate grounds in 2009, having been diagnosed with terminal prostate cancer, and died in the Libyan capital Tripoli in May this year. Prior to his release, he dropped an appeal against his conviction.
His death prompted fresh calls for an independent inquiry amid ongoing doubts over his trial.
The Scottish Government insists it lacks the powers to preside over a sufficiently wide-ranging probe, but the Crown Office is continuing to investigate the bombing in the hope of bringing others to justice.
Last night, the Scottish Government said: "It remains open for relatives of Mr al Megrahi or the relatives of the victims of the Lockerbie atrocity to ask the SCCRC to refer to the case to the Appeal Court again on a posthumous basis, which ministers would be entirely comfortable with."