His warning comes after UK officials sounded the alarm on Thursday night over the B.1.1.529 variant, which has the potential to evade immunity built up by vaccination or prior infection.
In a Covid-19 update to the House of Commons on Friday, Mr Javid said the B.1.1.529 variant could “pose a substantial risk to public health”.
Mr Javid said no cases of the new variant have yet been identified in the UK, but said the government was concerned it may pose greater risks than current strains.
He stressed the situation is “fast-moving”, and “there remains a high degree of uncertainty”.
“We are concerned that this new variant may pose substantial risk to public health,” said Mr Javid.
"The variant has an unusual large number of mutations. Yesterday the UK Health Security Agency classified B.1.1.529 as a new variant under investigation and the very technical group has designated it as a variant under investigation with very high priority.”
Mr Javid added: “Early indications show this variant may be more transmissible than the Delta variant, and current vaccines may be less effective against it.
"It may also impact the effectiveness of one of our major treatments.”
Discussions are ongoing over the prospect of adding further countries to the travel red list to reduce the risk of importation, the health secretary said.
He told MPs on Friday morning: “We are going primarily by where the new variant has been detected at this point, and that’s been confirmed in two countries in southern Africa – South Africa and Botswana.
“We’ve included the four other countries I mentioned earlier in southern Africa as a precaution.”
Mr Javid added: “We are keeping this under review and there’s very live discussions going on about whether we should and when we might add further countries, and we won’t hesitate to act if we need to do so.”
UK transport secretary Grant Shapps said the UK was “buying time” by adding countries to the list.
He told BBC Radio 4’s Today programme on Friday: “I think all the history of coronavirus suggests that it is best to act quickly, determine the extent of the way that the virus interacts with vaccines, treatments, transmissibility and then give yourself a bit more time.
“It is inevitable, of course, that it will go all around the world if it is going to do so.
“So this doesn’t prevent it from coming here, but it slows things up and gives us the chance to grow the cultures and test those questions about vaccines and treatments against it.”
England’s chief medical officer Professor Chris Whitty said there was a lot that was unknown about the new variant.
He expressed concern about further UK lockdowns if a new variant took hold, saying: “My greatest worry at the moment is that people … if we need to do something more muscular at some point, whether it’s for the current new variant or at some later stage, can we still take people with us?
The UK Government said as of 9am on Friday, there had been a further 50,091 lab-confirmed Covid-19 cases in the UK, the highest reported daily figure since October 21.