Taxpayers are paying millions of dollars to fund think tanks closely aligned to the major political parties.

Experts say voters should be concerned about the little-known Department of Finance grant payments to the Liberal-aligned Menzies Research Centre and Labor-aligned Chifley Research Centre.

Menzies Research Centre executive director Nick Cater has defended the grants. Credit:60 Minutes

The department has given the two think tanks, which have close financial links to their parent parties, more than $1 million each in grants since 2012, an analysis of department documents shows.

The department says it gives the money through its Grants-in Aid program to organisations that "advance public policy debate". But analysis shows 85 per cent of the program's money goes to party-aligned organisations.