Liberal Democrat ministers are battling what they regard as a Tory attack on "the very principle of trade unions" by refusing to scrap a system of collecting subscriptions from salaries.
Paymaster General Minister Francis Maude has asked all Whitehall Departments to consider ending the long-standing "check off" system.
But Lib Dem cabinet ministers have refused to implement the change in departments they head and junior colleagues are fighting the proposals elsewhere, a senior party source said.
Deputy Prime Minister Nick Clegg blocked Mr Maude from pushing the move through in the Cabinet Office.
A failed High Court challenge to the process by Communities Secretary Eric Pickles suggested the initiative could end up costing the taxpayer more than it saved and was politically motivated, they said.
Unions said the "reckless" legal case had cost the public purse £90,000 - while the system cost only £300 a year to administer.
The source said: "The Liberal Democrats have always believed that trade unions play a vital role in representing their members at work - in both the public and private sectors.
"Some Tories want to attack the very principle of trade unions and that is not something the Liberal Democrats will ever sign up to.
"This is petty party political point scoring of the lowest kind from the Tories.
"Their plans won't save any money at all - in fact they might cost the Government money in legal fees.
"This is classic pandering to Conservative Party's anti-union right.
"Nick Clegg has ensured that no Liberal Democrat led department will take part in this and Liberal Democrat ministers in other departments will fight against these unnecessary proposals."
Paul Kenny, general secretary of the GMB union, said: "Trade unions are attacked by the Conservatives because we speak up for people in the world of work and fight for a fairer society, and their paymasters don't like this as it clashes with their interests of low pay and exploitation.
"Free, independent trade unions are the benchmark of a democratic country."