In the past, the Cabinet Office has said the Government Procurement Card should only be used by departmental permanent secretaries.
Other Whitehall departments are said to have declined to provide such cards to political advisers.
Labour's Margaret Hodge, who chairs the House of Commons Public Accounts Committee, said: "I don't think any political appointee, minister or special adviser should be allowed to use the Government Procurement Card."
Jon Ashworth, a Labour backbencher, added: "Clearly, the Scotland Office has some questions to answer about what's going on here."
Last night, a spokesman for the Scotland Office told The Herald everything was above board.
He said: "The Scotland Office has offices in Whitehall and Edinburgh.
"In support of the Secretary of State, the special adviser's job means frequent travel between them and elsewhere as business dictates.
"The Government Procurement Card has been used infrequently, for work-incurred travel and accommodation costs only, and is fully and regularly audited by the Scotland Office."