Conservative MP Matthew Hancock wrote to the Charity Commission following reports that both War on Want and the Jubilee Debt Campaign were backing protests by the UK Uncut group.
UK Uncut has disrupted Vodaphone stores, including the flagship Glasgow shop, and is threatening similar action against Topshop and other stores in Sir Philip Green's retail empire in the run-up to Christmas.
Mr Hancock, who was Chancellor George Osborne's chief of staff before the general election, said the charities' endorsement appeared to breach guidelines on "political activity".
War on Want, which was founded in 1951, firmly rejected the suggestion it had done anything wrong, saying fighting tax avoidance had always been one of its "core" campaigns.
A spokesman added: "Mr Hancock would do well to look to the policies of the government which allow tax-dodging by rich individuals."