No one would be able to buy cigarettes without the permit, under the idea proposed by Health England.
Its chairman, Professor Julian Le Grand, told BBC Radio 5 Live the scheme would make a big difference to the number of people giving up smoking.
But smokers' rights group Forest described the idea as "outrageous", given how much tax smokers already pay.
Professor Le Grand, a former adviser to ex-PM Tony Blair, said cash raised by the proposed scheme would go to the NHS.
He said it was the inconvenience of getting a permit - as much as the cost - that would deter people from persisting with the smoking habit.
"You've got to get a form, a complex form - the government's good at complex forms; you have got to get a photograph.
"It's a little bit of a problem to actually do it, so you have got to make a conscious decision every year to opt in to being a smoker."
He added: "70% of smokers actually want to stop smoking.
"So if you just make it that little bit more difficult for them to actually re-start or even to start in the first place, yes I think it will make a big difference."
But Forest said it would be "an extra form of taxation, while tobacco taxation is already at record levels".
Forest spokesman Simon Clark said that when the cost of administration, extra bureaucracy and enforcement are taken into account, "the mind boggles".
He added that the people most affected by the proposals would be "the elderly and people on low incomes".
Mr Clark added: "The senior government advisor putting this idea forward is not only adding to the red tape and bureaucracy we already have in this country.
"He is openly bragging that he wants to make the form as complex as possible to fill in."
A department of health spokeswoman did not rule out such a scheme as part of the next wave of tobacco regulation.
She said: "We will be consulting later this year on the next steps on tobacco control.
"Ministers are seeking input from a whole range of stakeholders."