Millions of dollars in secretive union slush funds, training schemes, members' dues and MPs' resources are propping up Labor's dwindling union base and bankrolling damaging factional battles for delegates to the ALP.

A Fairfax investigation has unearthed cashed-up but little-known funds used to bankroll union elections and factional fights across the country.

It points to possibly unlawful misuse of union funds and union and parliamentary staff, including in the Health Services Union elections in Victoria in 2009 and 2012, and the Transport Workers Union's $500,000 takeover of its own Queensland branch in 2010 with the backing of disgraced former Health Services Union leader Michael Williamson.

In Victoria, the plumbers' union is under investigation by the Fair Work Commission over the spending of members' dues on the bitter 2012 HSU elections.