Rishi Sunak did not clear Home Secretary Suella Braverman’s article attacking the Metropolitan Police for its handling of pro-Palestinian protests.
The PM’s spokesperson said Downing Street is “looking into what happened” with the article.
But they added Mr Sunak had full confidence in the home secretary.
Writing in The Times, Ms Braverman accused the force of applying a “double standard” to its policing of protests.
She claimed aggressive right-wing protesters were “rightly met with a stern response”, while “pro-Palestinian mobs” were “largely ignored”.
Ms Braverman’s comments have been condemned by former police officers and MPs – with some calling for her to be sacked.
“It was not agreed by Number 10,” Mr Sunak’s spokesperson said, when asked if the article was signed off by his top team.
Labour leader Sir Keir Starmer said Mr Sunak’s government was led by an “out of control home secretary”.
Sir Keir accused the home secretary of undermining the police and said Mr Sunak was “too weak to do anything about it”.
Ms Braverman wrote the article after Mr Sunak held a meeting with Met Police commissioner Sir Mark Rowley to discuss security ahead of a pro-Palestinian march on Armistice Day on Saturday.
London’s police force has faced increasing pressure to prevent Saturday’s march from going ahead.
Police have said they expect a large rally on Saturday, the anniversary of the end of World War One, prompting fears of violent clashes with counter-protesters.
But Sir Mark has said the pro-Palestinian march may only be stopped if there is a threat of serious disorder, and that the “very high threshold” has not been reached.
In an article for The Times, the home secretary claimed that there was “a perception that senior officers play favourites when it comes to protesters”.
“Right-wing and nationalist protesters who engage in aggression are rightly met with a stern response yet pro-Palestinian mobs displaying almost identical behaviour are largely ignored, even when clearly breaking the law,” she wrote.
There have been regular protests in London calling for a ceasefire after Hamas gunmen launched an attack on Israel from the Gaza Strip on 7 October, killing more than 1,400 people and taking more than 200 hostages.
Israel has been carrying out strikes on Gaza since then in response and has now also launched a ground offensive. More than 10,500 people have been killed in Gaza, according to the Hamas-run health ministry, half of which are believed to be children.