Doctors have accused the government of meddling with the independence of the review body that decides their pay.
Doctors' pay is set by an independent panel
The British Medical Association is angry that Health Secretary Patricia Hewitt and Chancellor Gordon Brown both wrote to the Pay Review Body.
Mrs Hewitt recommended a pay rise of no more than 1%, while the chancellor said pay increases should be based on the government's 2% inflation target.
The Department of Health dismissed accusations of interference.
But the BMA said ministers' intervention was unacceptable and incompatible with the review body system.
The Department of Health had already submitted its formal evidence to the Doctors' and Dentists' Pay Review Body (DDRB) in October 2005. This recommended rises of no greater than 2.5%.
Mr James Johnson, the BMA chairman, has complained to Michael Blair QC, the DDRB chairman.
Mr Johnson said government interference "seeks to undermine the established process by which evidence is considered, and will provoke anger and further disenchantment among [BMA] members."
The BMA is concerned that the government is trying to blame doctors for current NHS deficits - and to minimise their pay increase as one way to tackle the problem.
It is calling on the DDRB not to be influenced by government pressure and to base its decisions in the usual way on the evidence submitted by doctors and the Department of Health.
Mr Johnson said: "These government recommendations are a kick in the teeth for doctors who have worked tirelessly to improve the quality of patient care and bring waiting times for operations down to record low levels.
"Doctors are as frustrated as patients by financial instability in the NHS; we're the ones struggling with limited resources to keep services running.
"Yet for all our hard work, the government is effectively saying that we should be punished for the failure of NHS managers to balance the books."
Mr Johnson added that as a result of European legislation, many junior doctors were already working more intensely for lower take home pay.
In addition, the government's old argument that juniors were guaranteed a job for life was no longer valid.
A Department of Health spokeswoman said it was "ridiculous" to describe the move as interference.
"The Treasury and Health Departments routinely give evidence to the DDRB.
"Following the submission of written evidence to the Pay Review Body, the Review Body invites each party to give oral evidence.
"The Secretary of State gave oral evidence on 12 December - her letter of 19 December was written at the request of the DDRB.
"As evidence to the DDRB, the letter was shared with the BMA and the DDRB invited the BMA to comment.
"Doctors have benefited hugely from our extra investment in NHS pay - earnings for hospital doctors have grown by 6.1% in 2004/05 which is considerably higher than the national whole economy average of around 4.0%."