The Catholic Archbishop of Glasgow, Mario Conti and the Rev Ian Galloway from the Kirk, made the appeal before a debate scheduled for Wednesday 2 September 2009.
MSPs (Members of the Scottish Parliament) are being invited to pass judgement on the decision, by the Justice Secretary, Kenny MacAskill, to free terminally ill Abdelbaset Ali Mohmed al-Megrahi.
The church leaders argue that the issue is a question of personal conscience because it depends on views of compassion which transcend party political considerations.
They say it would be wrong for party whips effectively to make the decisions on behalf of individual MSPs.
A spokesman for Archbishop Conti declared: "Parliament should be free to express itself on this issue without the interference of party whips."
Mr Galloway added: "I would hope it would not be decided by the parties, and MSPs would have the opportunity to reflect themselves on the issues."
Both men made it clear last week that they supported MacAskill's decision.
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