Reports had claimed the pair had the political campaigner and government adviser Nimco Ali spent time at Downing Street over the festive period.
London and the south east of England had been placed under strict lockdown rules just a week before Christmas.
At the time households mixing indoors was banned with socialising outside restricted to one other person.
Exemptions were in place for those in bubbles, while those living on their own were able to pair up .
After the US magazine Harper’s reported that Ms Ali “spent Christmas with the couple at No 10 despite pandemic restrictions on holiday gatherings”, Downing Street have now denied the claims.
A No 10 spokesperson said: “The PM and Mrs Johnson have followed coronavirus rules at all times. It is totally untrue to suggest otherwise.”
The spokesman indicated Ms Ali was in the Johnsons’ “childcare bubble” - which would have been allowed at the same time as a “support bubble” with Carrie’s mother.
Mr Johnson’s spokesman also denied Ms Johnson’s mother stayed for Christmas.
He said: “For the avoidance of doubt, I'm happy to confirm that the Prime Minister's or Mrs Johnson's mother were not there over the Christmas period.”
Downing Street did not deny specifically that Ms Ali spent the holiday with the Johnson’s.
Under the rules, the Johnsons would have been allowed to form a support bubble with a household of any size because they had a baby under the age of one.
People with kids under 14 were also allowed to form a ‘childcare bubble’.
Therefore the childcare bubble could be formed with a different person to whoever was in your support bubble.
The government guidance added: “You must avoid seeing members of your childcare and support bubbles at the same time.
“You can only use a childcare bubble for childcare. You cannot use a childcare bubble to mix with another household for other reasons.”
Responding to the allegations on Twitter, Ms Ali wrote: “No I did not break any rules but you knew that and just wanted a reason to tweet hate”.