Sir Mark Rowley said it was unfortunate those arrested could not protest, but he supported the officers' actions.
He said there had been a "concerning" threat to the Coronation.
People purporting to be stewards had white paint they wanted to throw to disrupt the procession, he said.
Sir Mark also said the Met had had growing concerns that protesters would use rape alarms, possible lock-on devices, loud hailers and vandalise monuments during the procession.
"Clearly, this would not only have been unlawful, but also extremely dangerous," he wrote in the Evening Standard newspaper.
A group of six anti-monarchy protesters, including the chief executive of anti-monarchy group Republic, Graham Smith, was arrested on the day of King Charles III's coronation under a controversial new law, the Public Order Act 2023.
They were held for almost 16 hours, later bailed and told on Monday that no further action would be taken against them.
Three women's safety volunteers who were arrested have also been released without charge.
Westminster City Council said in a statement on Tuesday evening that it had requested an apology from the police to the Night Star volunteers, who hand out rape alarms, and would continue to work with the force "to learn from this unfortunate incident".
Addressing the six anti-monarchy arrests in his newspaper article, Sir Mark said: "While it is unfortunate that the six people affected by this were unable to join the hundreds of peaceful protestors, I support the officers' actions in this unique fast-moving operational context."
Mr Smith has said he is considering legal action over the arrests, which he said followed four months of conversations with the Met about Republic's protest plans.
In total, 64 people were arrested in London during the Coronation policing operation. Police said 52 of these related to concerns people were going to disrupt the event. Four people have so far been charged.
Recent changes to the Public Order Act, passed just days before the Coronation week, make it illegal to prepare to lock-on - when a person attaches themselves to an object so they cannot be moved.
The Met expressed "regret" on Sunday evening after it found there had been no proof the six protesters with Republic had been planning to use "lock on" devices (equipment to attach themselves to objects), as had been claimed.
It said the six had had their bail cancelled and no further action would be taken.
Matt Turnbull of Republic, who was one of those held, said: "It is a concerning thing for everyone for the police to be able to determine that you may be about to commit a crime when there is no evidence of that to be had."
Former cabinet minister David Davis - who had been the only Conservative MP to vote against the changes to the law - told the Today programme the new law was "too crude and too broadly defined".
Speaking later in the House of Commons, Mr Davis pointed out that "within one week of the Public Order Bill entering the law", the Met had had to "apologise" over arrests.
SNP MP Joanna Cherry, who tabled an urgent question on the policing of protests at the Coronation, called for further investigation into the arrests and asked whether political pressure had brought to bear on the police.
In response, Policing Minister Chris Philp defended the police's actions, telling the Commons that "at the point the arrest was made, the police reasonably believed there were grounds to do so".
Mr Philp said hundreds of people had peacefully protested against the monarchy, adding that anyone unhappy with their arrest could make a complaint.
Labour MP Dame Diana Johnson, who chairs the Home Affairs Committee, said the committee would "no doubt" want to look at the use of the new law in the policing of Coronation protests.
The 2023 Public Order Act is the government's second major piece of legislation changing protest laws in under two years.
In 2022 MPs voted to place greater restrictions on public processions if they are too noisy.
The new act goes further:
• Protesters who interfere with "key national infrastructure" including roads and railways can face 12 months in jail.
• Anyone who fixes themselves to an object or building to create an immovable obstacle, a tactic known as "locking on", could be jailed for six months.
• The law bans protesters from committing acts of "serious disruption" - meaning demonstrations which prevent people going about their day-to-day activities.
• Other new offences include up to three years in jail for tunnelling as part of a protest. Police will also have new powers to search people for super-glues and padlocks.
Prime Minister Rishi Sunak defended the new legislation, telling broadcasters: "What the government has done is give the police the powers that they need to tackle instances of serious disruption to people's lives.
"I think that is the right thing to do and the police will make decisions on when they use those powers."
Labour leader Sir Keir Starmer said arrests at protests were a "difficult judgment call" for police but that "we need to protect legitimate protests".
However, Sir Keir refused to say that his party would scrap the Public Order Act, telling the BBC the law had not "bedded in yet" and that it was important to balance protecting peaceful protest with the need to police disruptive action.
London Mayor Sadiq Khan has said he has requested "further clarity" from Scotland Yard, saying the right to peaceful protest is an integral part of democracy.
Liberty, a campaign group which defends civil liberties, said the government had "rushed through" the Public Order Act ahead of the Coronation.
Sam Grant, advocacy director at the organisation, called for the Public Order Act to be repealed.
He said the police had been "overzealous" in using their "broad and poorly defined" powers - "with serious consequences for people's freedom of expression."
He added: "We should all be very worried about the impact this will have on our right to make our voices heard on the issues that matter to us."