A spokesperson said the decision had been taken because of the strict limit of 30 on attendance at the ceremony in Windsor Castle on 17 April under coronavirus regulations.
Mr Johnson took the decision not to attend in order not to take a space which could go to a member of the Duke of Edinburgh’s family.
“As a result of the Coronavirus regulations, only 30 people can attend the funeral of HRH The Prince Philip, Duke of Edinburgh,” said the spokesperson.
“The prime minister has throughout wanted to act in accordance with what is best for the Royal household, and so to allow for as many family members as possible will not be attending the funeral on Saturday”.
Campaigning for 6 May elections to local councils and the Scottish and Welsh parliaments has been suspended as a mark of respect to the Duke.
The House of Commons and the devolved assemblies in Cardiff and Edinburgh will be recalled on Monday to allow members an opportunity to pay tribute to the Queen’s consort of more than 70 years.