Rishi Sunak against changing flag design on England's Euro 2024 kits
The US sportswear firm revealed it had altered the cross, the flag of England, using purple and blue horizontal stripes in what it called a "playful update" ahead of Euro 2024, which starts in June.
Nike said the colours on the back of the collar - different from the traditional red cross - were inspired by the training kit worn by England's 1966 World Cup winners.
But the decision has led to a furious backlash from some fans and former players, with leading politicians adding their voices.
Sunak - a fan of Championship side Southampton - said he "prefers the original" England shirt.
"My general view is that when it comes to our national flags, we shouldn't mess with them," he told reporters. "Because they are a source of pride, identity, who we are, and they're perfect as they are."
Culture Secretary Lucy Frazer, whose remit includes sport, said the Football Association and its kit partner had failed to put supporters first.
"Fans should always come first, and it's clear that this is not what fans want," she said on X, formerly known as Twitter.
"Our national heritage - including St George's Cross - brings us together. Toying with it is pointless and unnecessary."
'Unifier'
Keir Starmer, the leader of Britain's main opposition Labour party and an Arsenal supporter, called on Nike to "reconsider" its decision to modify the St George's Cross.
"I'm a big football fan, I go to England games, men and women's games, and the flag is used by everybody. It is a unifier. It doesn't need to be changed. We just need to be proud of it," Starmer told The Sun newspaper.
"So, I think they should just reconsider this and change it back. I'm not even sure they can properly explain why they thought they needed to change it in the first place."
The debate over the new design comes with British politics in the grip of so-called "culture war" issues, pitting proponents of "traditionalist" values such as Sunak's ruling Conservatives against those with more liberal, "progressive" views.
Former England goalkeeper Peter Shilton, who is England's most-capped player, told the BBC that he does not agree with the changes, describing himself as a "traditionalist".
"We have so many changes to kits these days so it really makes fans buy fresh kits to stay up to date and it is very expensive," he told the BBC. "It is a colour difference and I think it is significant.
"Once you start changing colours there is no end to it. There is no need to change the colour of the flag."
A Nike spokesman previously told media outlets: "The England 2024 home kit disrupts history with a modern take on a classic.
"The trim on the cuffs takes its cues from the training gear worn by England's 1966 heroes, with a gradient of blues and reds topped with purple. The same colours also feature an interpretation of the flag of St George on the back of the collar."