Delegates at the conference voted on the motion "This meeting has no confidence in Andrew Lansley, the Secretary of State for Health, and calls for him to resign".
The motion won by a slight majority, with 158 delegates voting in favour and 124 against.
Dr Gary Marlowe, who presented the motion, told the conference: "I do not trust this man."
Dr Marlowe accused Mr Lansley misleading doctors and the public during the election over his plans for the Health and Social Care Act, which became law in March after a tortuous passage through Parliament.
He said: "During the election, there was no mention of a specific direction and/or any detail of the NHS reforms. By all accounts Mr Lansley has a long and detailed knowledge of the NHS and has been working on his plans throughout opposition. It is clear that during the election he mislead the public and the profession."