Some suggest the row over Ms Gray's pay has exposed the chaos inside Labour's Downing Street operation just weeks after the party swept to power at the General Election.
The Conservative Party responded with a series of questions for Labour, including whether the PM personally signed off on Ms Gray's new salary and the increase to the cap on the highest pay band.
They also asked whether a special adviser remuneration committee still exists and if Ms Gray is a member, as well as what role she played in setting her salary and changing pay bands.
Sir Keir claimed he was completely in control in the immediate aftermath of the revelation about Ms Gray's pay. Since then, members of his Cabinet team have sought to defend Ms Gray and respond to anger over gifts handed to Labour MPs by wealthy donors.
Angela Rayner said she rejected the suggestion the Prime Minister's chief of staff was "part of a problem", telling the BBC: "I don't accept that Sue Gray is part of a problem at all and I don't accept the caricature of how Number 10 is working."
The Deputy Prime Minister pointed to work on the Government's legislative agenda and responding to the Grenfell Tower Inquiry's final report as cases where she, the Prime Minister and Ms Gray had all worked together.
She added: "I'm in Number 10, I go in at 8.30 every single morning and I do not see that, and I do not see this caricature that somehow we're all fighting over mansions or all at loggerheads with each other.
"Actually, we're all really focused on making sure we deliver because that's what the people are going to ask in a few years' time - is Labour changing the country for the better? - and we are determined to make sure we answer that question."
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