The chief medical officer, Sir Liam Donaldson, told MPs yesterday he had come close to resignation over the government's failure to back a complete public smoking ban as a Department of Health consultation found near-universal support for a ban in all pubs and clubs.

As MPs prepare for the legislation's second reading next week, Sir Liam told the Commons health select committee that the government's decision to ignore his advice had left him in a "very difficult position." He added that as it stood the government's proposal was likely to widen health inequalities between rich and poor.

"I have had to think hard about what I want to do about that position," Sir Liam told the committee. "There are some areas where if your advice is ignored and it damages the public health you would have to consider resignation".

He believed it was better for him to stay in his post and use the position to press for a complete ban.

Sir Liam told the committee his strong advice had been ignored by ministers. It was the first time in his seven years that this had happened. Legislation, published last month, bans smoking in most public places but after a last-minute cabinet battle allows smoking in private clubs and pubs not serving food.

Sir Liam's remarks fuel the prospect of a Labour rebellion on the issue when MPs vote on details of the bill shortly after Christmas. Labour rebels, Liberal Democrats and some Tories are expected to back an amendment introducing a full ban.

Kevin Barron, chairman of the health committee, described Sir Liam's as "a remarkable and brave statement." Although the health committee is yet to complete its investigation, its report is expected to criticise the compromise ban.

The Department of Health played down the significance of Sir Liam's remarks, saying that he was only one of a number of advisers feeding into the policy.