Sir Liam Donaldson said the Government was expecting the number of cases to rise in the autumn but it was difficult to predict the timing with accuracy.
Some experts have said the swine flu cases will surge in September and October when schools and universities go back after the summer break.
Sir Liam's comments come as figures released today show a continuing fall in the number of people newly diagnosed with swine flu, with an estimated 11,000 new cases in England last week.
This is down on the 25,000 new cases estimated for the week before.
The data shows a drop in the number of cases across all age groups and in most parts of the country.
There are 263 patients being treated in hospital in England, of which 30 are in intensive care, down on the 371 (39 in intensive care) reported last week.
The number of deaths linked to the virus stands at 54, with almost half of those (25) having died in London.
Last week, the number of confirmed deaths was 44. There have been five additional deaths in Scotland.
Also today, Sir Liam said just one in 10 people reporting flu-like symptoms to their GP or the National Pandemic Flu Service for England actually do have swine flu.
This is down on the figure of around one in four from several weeks ago, although Sir Liam said the drop was to be expected.
Monday tends to be the day of the week when the Pandemic Flu Service sees the highest levels of activity.
Sir Liam said he could speculate on the timing of the second wave of swine flu but it was "virtually impossible" to predict with any accuracy.
He said he hoped the current pandemic would follow the pattern of a pandemic in 1968/70, when the second wave hit around Christmas time.
This would give the UK time to vaccinate as many people as possible and possibly avoid a peak altogether, Sir Liam said.
The Government announced the list of priority groups for the vaccine last week, starting with people in high risk groups such as those with asthma and diabetes. The programme is expected to start in October.
Sir Liam made it clear that a second wave of swine flu is definitely expected, adding: "Our best guess is that it will be in our flu season this autumn and winter."
Asked if the figure announced by Health Secretary Andy Burnham earlier this year - that the UK could see 100,000 new cases a day by the end of August - needed to be revised, Sir Liam said Mr Burnham had been working from the best available scientific evidence at the time.
That figure is in the process of being revised by the Scientific Advisory Group for Emergencies.
Sir Liam said experts could not be sure that the drop in new cases was just down to schools closing for the summer break. The climate had also changed with the warmer summer months, he added.
"It won't be national policy to close schools across the whole country or stop them going back - we don't think that would have very much impact," he said.
But he said some schools may close in individual parts of the country if necessary.
Sir Liam said the full picture on how swine flu has affected the UK, including number of excess deaths, would not be known until after the pandemic had passed.
He said the UK had taken a much more "aggressive policy" towards tacklingg the disease than some other countries in that the Government used school closures and gave anti-virals preventativelyy to people who had come into contact with swine flu victims.
"It's difficult to tell at this stage how much difference that made but certainly that containment phase we ran for a long time," he added.
Most people with swine flu are still experiencing mild symptoms, although around one in five deaths is among previously healthy people.
Sir Liam said it should "not be taken lightly" as people were still in hospital.
"Although the numbers are falling this is very exceptional at this time of year to have people with flu in hospital and intensive care units."
A spokesman for the Health Protection Agency said: "One of the ways the Health Protection Agency monitors the level of flu circulating in the community is by lab testing swabs from a sample of patients with flu-like illness visiting their GP or calling the National Pandemic Flu Service.
"This gives us a good indication of the proportion of patients with a flu-like illness who actually have flu, rather than another virus.
"Current sampling suggests that the proportion of patients presenting with flu-like illness who have swine flu has fallen to below 10 per cent.
"This pattern is typical of what we see during the winter flu season when circulating flu levels fall.
"At the height of a typical flu season, this proportion usually reaches levels of around 50-55 per cent."
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