The document, acquired by a well-placed US source, threatens to undermine US President Barack Obama's claim last week that all Americans were "surprised, disappointed and angry" to learn of Megrahi's release.
Scottish ministers viewed the level of US resistance to compassionate release as "half-hearted" and a sign it would be accepted.
The US has tried to keep the letter secret, refusing to give permission to the Scottish authorities to publish it on the grounds it would prevent future "frank and open communications" with other governments.
The note added: "Nevertheless, if Scottish authorities come to the conclusion that Megrahi must be released from Scottish custody, the US position is that conditional release on compassionate grounds would be a far preferable alternative to prisoner transfer, which we strongly oppose."
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