The Times newspaper claimed last week that the parliamentary inquiry into the leaking of more than a million documents was "focused" on the role of the Williams Lea subsidiary.
However, a spokesman for the company said that it was certain that there had been no breach of security at the company.
The company said it has conducted a thorough internal investigation with the help of an external auditor and it could find no "no trace of a breach" in security.
It added: "TSO has an impeccable record for security and we will not hesitate to take the appropriate action should anyone attempt to damage our reputation with unfounded allegations."
The claims by The Times were prompted by an unnamed parliamentarian source who said that the data only existed in a consolidated format at TSO.
MPs' expenses have been at the centre of a parliamentary-wide scandal following the leaking of the documents prior to their intended publication in edited form this summer.
John Wick is known to have been the intermediary who brokered the sale of the files to The Daily Telegraph, which published details of the expenses, although he has denied that he was the original source of the leak.
TSO 'absolutely certain' of no involvement in MPs' expenses leak
The Stationery Office (TSO) has said that it is 'absolutely certain' it was not involved in the leaking of MPs' expenses claims.