The union Community, which is also a major Labour Party donor, has been told by Her Majesty's Customs & Revenue (HMRC) to hand over documents relating to the pay and expenses of its senior staff, including former general secretary Michael J Leahy.
Details emerged last month in a tax tribunal judgment that upheld a fine against Community for failing to disclose information to HMRC.
Community, which has its roots in the Iron and Steel Trades Confederation, has given the Labour Party £1.5 million since its creation in 2004. About 10% of its 30,000 members are in Scotland, including four Labour MSPs.
In July last year its UK conference voted to join Better Together, and the union now expresses "concern" at Scotland leaving the UK.
The union's dispute with Her Majesty's Customs & Revenue dates back two years to an audit of its PAYE and National Insurance Contribution (NIC) records, which prompted HMRC to raise "a number of issues" and make a detailed follow-up request for more information, which Community challenged. In September 2012, HMRC issued an "information notice" obliging Community to comply.
The judgment states HMRC wanted to establish whether Community had tax liabilities in about a dozen areas, including chauffeur benefits; cricket club membership; "leaving meals"; the "unreceipted expenses" of union officials; and Michael J Leahy's "self-authorised" expenses claims, "private items and cash withdrawals".
Community later supplied some information, but not all of it, so HMRC fined the union £300.
Community then appealed the fine and information notice, but the appeal was dismissed last year.
The union has until the end of February to lodge an appeal to a higher tribunal.
Leahy retired in late 2013, and was replaced as general secretary by Roy Rickhuss.
Community said: "We have now complied with HMRC's request and given that the information provided is still being studied by HMRC.
"We are not in a position to make further comment."
Better Together and HMRC declined to comment.