Ms Hewitt was appearing before the Common's Health Committee as the Health Bill, setting out the smoke-free legislation, was published in Parliament.
She acknowledged differences of opinion among Cabinet members, but said they had agreed to fulfil their clear manifesto commitment.
Giving evidence to the committee, Ms Hewitt acknowledged Cabinet divisions had forced the Government to look again at the proposals.
"We discussed it between ourselves and we agreed that since any way forward has both advantages and disadvantages, we would continue on the lines that we set out so clearly in the manifesto only five months ago, but with this further consultation on how we give the bar staff in the exempt pubs and membership clubs as much protection as we can, quite possibly through the creation of the separate smoking areas or rooms," she said.
The partial ban, which exempts private members' clubs and pubs that do not serve food, was seen as a defeat for Ms Hewitt who pushed for tougher measures and had publicly described the proposals as "unworkable".
Meanwhile, Downing Street denied Tony Blair's authority had been undermined by Cabinet infighting over the smoking ban.
The Prime Minister's spokesman said that he had been concentrating this week on the "big picture" issues, such as education reform and the future direction of the European Union.
"On the big issues of the day, the Government is taking radical and important decisions," the spokesman said.
In her appearance before the committee, Mrs Hewitt repeatedly emphasised that the measures proposed were "a very significant step forward", adding that it was only a matter of time before a complete ban was instituted.
She was grilled by the committee of fellow MPs, one of whom told her "to most people it is a confusing mess that is extremely difficult to police".
But she admitted that the partial ban was "not perfect" and also that there had been divisions in Government over the details.
She told the committee: "This is a very significant step for public health and a very significant step towards the complete ban that I know you and many others would like to see."
She said public consultation had shown around 90% supported legislation, and while there were of course some who didn't believe Government should legislate in the area at all, the "great majority of those supporting legislation would like us to go that extra step further and ban smoking in drink-only pubs".
The Health Secretary agreed that one of the problems with policy making the distinction between pubs serving food and those that didn't, is that there were more non-food pubs in poor communities.
Pressed on whether the Bill did not address health inequalities, she said: "I do believe from the evidence...we will see more non-food pubs in poorer areas than in more affluent areas.
"That is, as I said earlier, one of the disadvantages between drawing a distinction between food and non-food but if we didn't, we would have other disadvantages. There isn't a perfect way forward."
Mrs Hewitt, who is believed to supported a total ban, was asked if she had been "rolled over by others" to bring in the partial measures.
She said she completely disagreed, but revealed there had been disagreements on the policies within Government.
When they looked at the manifesto and the very difficult balance they were trying to strike between protecting employees and respecting the rights of the minority, "to do something that is perfectly legal", it was decided the right balance was the one contained in the manifesto - although there were disadvantages which ever way they went.
"We had complete agreement across 99% of the policy. We had disagreement on the specific issue on the pubs that don't serve foods, so we did what any sensible organisation would do, and we discussed it. We were all in complete agreement, and agreed to go forward on the basis of the manifesto."
She told the committee that currently about 50% of the workforce had a smoke-free environment, but the measures proposed would increase that to 99%, so 12 million more workers would be included.
She had brought forward the legislation to come into force in the summer of 2007 and envisaged the legislation would be largely self-enforcing.
And she added: "I have said both this morning to the committee and the BMA, I think it is only a matter of time before there is a complete ban and that 1% of workers in non-food pubs will also be included."Reuse content