On the day it was announced that everyone aged five and over is now eligible to be tested for coronavirus if they are showing symptoms, Jonathan Van-Tam said the available data showed children were not "high output transmitters" of the disease.
He told the daily Downing Street press briefing: "The emerging data from around the world on the whole suggests that the rate of infection in children is about the same as in adults, possibly a little lower in the younger age children, but they get this much more mild disease, on the whole.
"The next question then is, can children transmit the virus to adults and here, we have to acknowledge that we're working with a new virus, where the data are pretty sparse at the moment.
"But the experts have already had a look at this and formed a conclusion that, unlike influenza like flu, where we are very clear that children drive transmission in the community to adults, it really does not seem to be the same kind of signal with COVID-19, that children are not these kind of big high output transmitters, as they are with flu.
"And then to the final point about getting children back to school and is that safe in terms of the R0, all of the measures that are being considered are always run against the test case of can we keep control of the R0.
"And if the answer is yes, then it will be considered. If the answer is it's going to risk pushing the R naught, higher than one, then our science advice to ministers will always be. No, we advise against it. As simple as that."
As part of efforts to ease lockdown restrictions, the Government wants to re-open some schools as early as June 1, though the measure has prompted strong opposition from teaching unions.
One of the main concerns is that having young children in close contact with each other and school staff will speed up the spread of the disease.
The Department of Health said today that 34,796 people had died in hospitals, care homes and the wider community after testing positive for coronavirus in the UK as of 5pm on Sunday, up by 160 from 34,636 the day before.
In the 24-hour period up to 9am today, 100,678 tests were carried out or dispatched, with a total of 67,409 people tested and 2,684 positive results. Overall a total of 2,682,716 tests have been carried out, and 246,406 cases have been confirmed positive.
According to latest figures, there have now been 2,285 coronavirus deaths in Yorkshire. The total has risen by 19 according to Monday's figures.
Earlier, it was announced that everyone aged five and over is now eligible to be tested for coronavirus if they are showing symptoms, which have been expanded to included a loss of taste or smell.
Health Secretary Matt Hancock drastically increased the number of people who can get tested for Covid-19 across the UK on Monday, with the Government trying to track the spread of the disease in order to ease the lockdown.
His announcement in the House of Commons came after the chief medical officers added the loss of, or noticeable change to, taste and smell to the NHS's list of coronavirus symptoms, weeks after experts first raised concerns that cases were being missed.
Anyone suffering the newly-added symptoms, or a continuous cough or high fever, should self-isolate for seven days to risk the spread of infection, and anyone they live with should stay home for 14 days.
Previously only essential workers, the over-65s and individuals who live with them could apply for coronavirus testing on the NHS website if they were showing symptoms.
But Mr Hancock told MPs that this was being expanded with immediate effect.
"I can announce to the House that everyone aged five and over with symptoms is now eligible for a test," he said.
"That applies right across the UK in all four nations from now."
Prof Jonathan Van-Tam said very few Covid-19 patients experience loss of taste and smell as a lone symptom of the virus.
Asked whether the UK had missed diagnosis of coronavirus by failing to add it to the list of symptoms to watch for until this week, the deputy chief medical officer said: "What I can tell you is from the Public Health England data set, called the FF100 - the first few hundred cases - there are actually 229 cases in there, all laboratory-confirmed Covid, all of whom have been studied in considerable detail and 0.44% reported anosmia on its own as a symptom.
"So, the point about anosmia is it doesn't always come as the first symptom.
"Even if it does, it is followed by the cough, the fever and many of the other symptoms I have talked about, referring to the WHO definition.
"So you don't miss those cases. The important thing was to work out if this would add any sensitivity to the diagnostic cluster we were using and the answer is that it makes a small - a very small - difference and we have therefore decided to do it."