The umbrella group for nearly 630,000 Scottish trade unionists has suggested a tranche of the money currently going directly to the UK-wide TUC should come north.
The STUC slipped into deficit by £22,578 in 2012. It believes a substantial increase in resources is needed, partly because more powers are being transferred to Holyrood.
One union source said there was going to be a stand-off between the two bodies.
Founded in 1897, the STUC is the collective voice for its 37 affiliated unions.
It played a key role in opposing the poll tax and was instrumental in the cross-party movement that led to the creation of Holyrood.
However, some trade unionists believe the body's post-devolution profile has not been high enough.
The Sunday Herald can reveal that the STUC, which will hold its annual congress this month, has circulated a paper to members about its "organisational effectiveness".
Part of the document is about the mechanism that determines how much funding the STUC and TUC receive.
Affiliated unions pay £1.29 to the STUC for every member in Scotland, while the UK-wide TUC receives a much more substantial £2.62.
Although affiliates receive services from both bodies, some trade unionists north of the Border believe the imbalance is outdated.
The STUC paper stated affiliation fee income was insufficient, adding: "The services provided by the STUC are increasingly of more relevance to union members in Scotland than those provided by the TUC, although our common affiliates pay twice as much per member in Scotland to the TUC than they do to the STUC."
Three changes have been suggested: affiliates increasing their fee to the STUC; the TUC handing over a chunk of funding; or changes to the formula that sees the UK-wide body receive more cash per head.
The last option would require agreement by both bodies but is unlikely to be welcomed by the TUC.
One of the reasons cited for a rethink is so the STUC has the capacity to deal with extra powers coming to Holyrood.
The paper claims that the STUC has been unable to take full advantage of the opportunities presented by devolution.
Its authors stated: "Although some significant advances have been made in the STUC's policy agenda since devolution, the General Council is well aware that it has far from maximised the opportunities available to influence policy in devolved and reserved areas to further advance the interests of working people."
A senior union insider said a stand-off loomed, but cautioned: "When thousands of workers are under pressure, the last thing they need is for the two organisations representing them to be fighting with each other."
STUC general secretary Grahame Smith said: "This is an issue that has been under consideration for some time by the STUC and its member unions at Scottish and UK levels.
"In recent years devolution has led to increased divergence of Scottish and UK policy on key issues. This has placed additional demands on the resources the STUC requires to represent its members' interests effectively in its engagement with the Scottish and UK governments and parliaments, industry and civil society."
A TUC spokesperson said: "Any decisions about TUC funding are made by the TUC executive and General Council, who have not seen this paper."