Suella Braverman was accused of being in "complete denial" after she claimed on Sunday it was unfair to say the huge hold-ups at Dover were "an adverse effect of Brexit".
Despite recurring problems with gridlock in Kent in 2021 and 2022, the home secretary claimed checks were "operating very smoothly at the border" - blaming current woes on bad weather and it being "a very busy time of year".
But Mr Sunak's official spokesperson said "a combination of factors" were to blame, including new passport control processes, poor weather and the high volume of traffic at Easter.
Asked about the role of post-Brexit checks, the spokesperson acknowledged that French officials are now required to inspect and stamp every passport as passengers leave the UK.
"Obviously we recognise there are new processes in place," they said on the manual checks.
"That's why authorities were given a long time to prepare for the new checks including during the transition period, of course, and we are in discussion with our French counterparts about how we can further improve the flow of traffic."
The No 10 officials said the government was "working with our French counterparts in increasing our ability to move traffic and passengers through freely".
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