All of Number 10's mobile phones have "auto-delete" functions on them which erase messages automatically, the Government has admitted.
The news means that potentially embarrassing messages between officials over the appointment of Peter Mandelson as the UK ambassador to Washington could have been erased automatically.
It comes as Prime Minister Sir Keir Starmer dismissed claims of a cover-up over former chief of staff Morgan McSweeney’s stolen phone as "far-fetched".
Cabinet Office minister Nick Thomas-Symonds said that it was incumbent on the advisers to copy WhatsApp messages onto "official government systems".
Tory shadow minister Mike Wood asked Cabinet Office minister Nick Thomas-Symonds in the Commons earlier this year "whether No10 special advisers have auto-delete functionality turned on for (a) corporate and (b) non-corporate communication devices when discussing government business".
Mr Thomas-Symonds replied: "Corporate communications channels have auto-delete functionality enabled."
Morgan McSweeney announced his resignation following the Peter Mandelson scandal
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He added: "Any government business that needs to be recorded must be copied onto the official systems."
Alex Burghart MP, Shadow Chancellor of the Duchy of Lancaster, said: "This whole affair stinks from nose to tail.
"The idea that key communications can simply vanish behind 'auto-delete' settings raises serious questions about transparency and accountability at the heart of Government.
"It only deepens the suspicion that Mandelson’s appointment was a backroom deal, stitched together by his protégés, rather than a decision made in the national interest."