Sir Bernard Hogan-Howe told a meeting at City Hall he wanted better organisation to reduce the number of officers involved in stewarding.
About 6,000 officers were deployed to the carnival on Saturday and 7,000 on Sunday on the August bank holiday.
Westminster and Kensington authorities agreed stewarding was an issue but public safety "was paramount".
But, Sir Bernard said he thought the street festival in west London could be "cheaper and safer".
At the meeting of the Mayor's Office for Policing And Crime (MOPAC) on Thursday, he said he would be writing to Westminster council and the Royal Borough of Kensington and Chelsea, where the carnival takes place, to advise them that he expected "more action".
He said: "We are writing formally to the local authorities... to indicate our lack of confidence at the moment in the quality of the organisation which is leading to policing having to fill the gap  - we can't take responsibility for the event."
He cited budget cuts as one of the reasons, as officers received double their daily salary on a bank holiday - meaning it cost more than £6m to police the event.
The force has previously said it is expects to make cuts of £800m by 2019.
"We have been talking for many years trying to get improvement and my judgement is it is producing limited effect - the risk to public safety remains and we cannot continue to provide policing at that level," he said.
Stephen Greenhalgh, deputy mayor for policing and crime, said: "We want a safe carnival and we want one that has a secure future and at the moment an event that is under-stewarded and over-policed is something that has to change."
A spokesman from the Royal Borough of Kensington and Chelsea said: "All the other agencies, ourselves included, must of course listen very careful to any proposals they may have for reducing the cost of policing carnival, but any changes must be consistent with the safety of the public."
A Westminster City Council spokeswoman said: "We do agree that the public purse, either our budget or the Police's, should not be spent on stewarding the carnival however we do believe that security and public safety should be paramount."
More than 400 people were arrested at this year's Notting Hill Carnival, with offences ranging from possession of an offensive weapon and assault, to theft and drugs offences.
A 17-year-old was also given a six-month detention and training order for wounding and possession of a knife with intent to cause threats and violence at the event.
Current levels of policing at the Notting Hill Carnival cannot continue, the Met Police commissioner has said.