Mr Mackinlay explained his decision to support the Prime Minister in the Conservative Party's recent confidence vote, in conversation with GB News' Gloria de Piero.
Appearing as Gloria's guest on The Real Me, the former deputy UKIP leader said there are "a number of factions at play" pointing to the complexity behind the party's internal politics.
The MP for South Thanet, 55, said: "You've got some who just don't like Boris – there's a number who just never liked Boris throughout his political career; then you've got others who are concerned about Brexit – they're still fighting the Brexit War."
He went further still, claiming that some MPs – who he did not name – called for the UK to go back into the EU's Single Market.
Tory MP for South Thanet Craig Mackinlay
GB News
Mr Mackinlay spoke to GB News' Gloria de Piero
GB News
He continued: "Then you've got those who have been shuffled out of Government, or those who think they're so marvellous they should be in Government.
"And then you've got those, who I would normally be quite aligned with, and that would be like your Philip Davies’ view of the Conservative Party, that we're not really delivering enough conservative policies.
"But, overlaying all of that, we've got a Brexit battle."
Mr Mackinlay told Gloria the Tories have always been a "very wide and broad church" and claimed Partygate "didn't have much to do with" the calling of the confidence vote.
He said: "It became that sort of culmination of all those that have got these negative feelings, and it sort of burst forth, and the 54 threshold to Sir Graham Brady was reached, and we had that vote last week.
"Of course nobody's sure what everybody voted but I voted to support the Prime Minister because, in my view, he's the best on offer."
Gloria then probed: "Do you honestly think there is a movement, or that part of the confidence vote in Boris Johnson is motivated in your party by a desire to overturn Brexit?"
And he replied definitively, saying: "Soften Brexit, I'm sure. Absolutely soften Brexit.
"There are some who would like us back in the Single Market and a closer orbit with the European Union.
"I'm sure once the Northern Ireland Protocol Bill actually goes to second reading and beyond through the subsequent stages of it, I think we'll see very clearly who they are."
Gloria probed Mr Mackinlay on the inner workings of the Tory Party
GB News
When asked what his message to such MPs would be, he replied: "Let's get on with this job.
"Let's make the best of Brexit opportunities, which I would say we have not really taken advantage of.
"I think we've got a civil service against a lot of these measures so that we don't diverge and use those freedoms fully, but I would say: ‘Please, let's get on with this job.'
"We were elected to get Brexit done. We're elected with a very, very big majority, a handsome majority that we don't see very often, and we have the opportunity to make Britain a better place.
"I do recognise that Covid put a lot of things on ice, and we've only got two years left before the next election."