A multibillion pound plan for radical change in the NHS could be derailed by No 10's insistence on new working practices at foundation hospitals.

Brendan Barber, the new general secretary of the Trades Union Congress, warned last night that the reforms intended for the whole system were in jeopardy because of the determination of ministers to introduce them without agreement at the new independent NHS trusts.

Speaking ahead of next week's annual congress of the TUC, Mr Barber said the Government was breaking an agreement by insisting the new flexible approach was adopted for foundation hospitals.

Unions have provisionally signed up to the reforms, the most far-reaching yet attempted in the public sector, provided they are tried out initially in 12 NHS trusts. However, ministers are insisting the changes are introduced from day one at foundation hospitals, which will have greater scope for determining their own employee relations policies.

The TUC leader said the decision could "destabilise" the whole programme of reform. He accused the Government of failing to think coherently on the subject and urged ministers to "get their act together".

The issue is expected to dominate the deliberations of the Public Services Forum, a mechanism agreed on Tuesday by the Prime Minister, which is aimed at giving unions an input into policy formation.

Mr Barber said there was "enormous frustration"with government policies that would be voiced at next week's congress in Brighton. The alliance with President George Bush in Iraq had contributed considerably to the negative mood about the Prime Minister. Trying to influence the Government was like trying to turn round a supertanker,Mr Barber added.