The chief medical officer Sir Liam Donaldson says he considered resigning over the government's refusal to back his call for a full ban on smoking.
Sir Liam decided to stay in place so he could push for smoking in all enclosed public places to be outlawed.
He said ministers had backed a partial ban to avoid being accused of running a "nanny state". But eventually there would be an outright ban, he predicted.
It was the first time his advice had been ignored, he told MPs.
Sir Liam, questioned by MPs on the health select committee, said in some respects a partial ban would be worse for health inequality, than no ban.
The government wants to ban smoking in all enclosed public spaces in England, except clubs, and food-free pubs.
Last month there was debate in Cabinet over possibly pushing ahead for a ban without exemptions, but after days of behind-the-scenes argument that proposal was rejected.
Sir Liam said the fact his advice had been ignored "put me in a difficult position".
He said: "I have had to think hard about what I want to do about that position.
"There are some areas where if your advice is ignored and it damages the public health, you would have to consider resignation if you were in my position.
"I have thought very very carefully about that. And my feeling is that I've championed this so far. When I produced my first annual report in 2002 nobody was calling for it to happen.
"I've pushed it so far. I've re-emphasised it in my 2003-2004 report. I have spoken publicly in opposition to the government policies on this one area which is an unprecedented position for a chief medical officer.
"And therefore my feeling is that this will eventually come and it's more likely to come if I stay in my post and continue to champion it."
Public health minister Caroline Flint said the government did "listen to the advice" of the chief medical officer and other organisations, but said it also had to "make choices about how we develop the work we are doing".
"We had to balance both the health issues and what the public was saying about where they thought the priorities were, and recognising that smoking itself is not an illegal activity," she told the committee.
But Conservative health spokesman Andrew Lansley said Sir Liam's comments were embarrassing for the government.
Charlotte Atkins, a Labour member of the committee, criticised the government for sending mixed messages.
Meanwhile the full results of the public consultation on smoking in England have also been released after Cancer Research UK requested them under Freedom of Information rules.
Professor Alex Markham, chief executive of Cancer Research UK, said: "This document confirms that support for comprehensive smoke-free legislation was overwhelming."
It shows that 90% of the 57,000 replies were against exempting pubs not serving food from a smoking ban.
More than 80% suggest the idea of a one metre smoking exclusion zone from the bar in non-food pubs is ineffectual and unenforceable.
The consultation shows that Primary Care Trusts believe areas of deprivation are the most likely ones to have non-food pubs.
This means, they say, their efforts to reduce health inequalities will be made harder.