Chief Medical Officer, Professor Sir Liam Donaldson, said on Thursday that the government's proposal to allow smoking in pubs in England, where no food is served, was unworkable.
"It is rare for the government to ignore the advice of its Chief Medical Officer or fail to act on it," Donaldson told a committee of lawmakers responsible for health matters.
"In the seven years I have been in post, this is the first situation I have encountered in which it has happened."
"It put me in a difficult position and I have had to think hard about what I want to do about that position."
According to newspaper reports, Blair's cabinet was sharply split over the extent of a ban.
Donaldson said he eventually decided to stay on in his job in order to fight for the imposition of a blanket ban.
"There are some areas where if your advice is ignored and it damages the public health you would have to consider resignation," he 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"
Sir Liam Donaldson,
chief medical officer
"I thought very, very carefully about that and my feeling is I have championed this so far ... I have spoken publicly on my opposition to government policy on this one area."
Donaldson told the committee that the government's proposals, which must still be passed by parliament, were unworkable and would increase health inequalities.
Pubs in disadvantaged areas and the poorer north of England were least likely to serve food and therefore most likely to allow customers to continue smoking, he said.
Donaldson said he believed Britain would eventually impose a total smoking ban, "and it is more likely to come if I stay in my post and continue to champion it."