Sadiq Khan has said he was not made aware that police were going to impose a ban on Extinction Rebellion protests on the streets of London.
The mayor of London said he had asked police to "find a way for those who want to protest the climate emergency to be able to do so legally and peacefully in London".
It comes after activists from the climate change group said they were launching legal action.
Mr Khan said on Tuesday evening that police had assured him protesters could still demonstrate "legally and peacefully" - indicating they must confine themselves to Trafalgar Square.
There has been growing criticism of the ban, made under public order laws.
In defiance of the police order, activists continued protests in the capital, targeting the Department for Transport.
The group's co-founder, Gail Bradbook, was arrested after staging a protest on the roof of the building over the HS2 rail link and airport expansion.
Nearby, on Millbank, demonstrators locked themselves to a caravan, prompting more arrests.
Tobias Garnett, a human rights lawyer working for Extinction Rebellion, said the group would be filing a High Court claim challenging the ban on the grounds it is "disproportionate and unlawful".
He said the group was seeking a fast-track hearing.
Mr Khan said in a Twitter statement: "Neither I nor the Deputy Mayor for Policing and Crime was informed before the Metropolitan Police took the operational decision to impose a Section 14 order on Extinction Rebellion Autumn Uprising last night.
"I've met with senior officers today to seek further information on why they deemed this necessary."
Under the current order, any assembly - a gathering of two or more people - linked to the Extinction Rebellion "Autumn Uprising" in London is unlawful.
Deputy Assistant Commissioner Laurence Taylor said the ban was imposed due to "continued breaches" of the condition limiting the demonstration to Trafalgar Square.
He added: "I want to be absolutely clear, the conditions put in place yesterday afternoon do not in any way ban protests from London, nor do they ban the activities of Extinction Rebellion as a group.
"These conditions specifically state that any assembly linked to Extinction Rebellion's 'Autumn Uprising' must now cease.
"The decision to impose further conditions was made in order to help us get London moving again.
"It is a lawful decision which we felt is entirely proportionate and reasonable to impose after nine days of sustained, unlawful assembly and protest by Extinction Rebellion."
Home Secretary Priti Patel tweeted her support of the police, saying: "Officers from around the country have done a fantastic job policing XR protests. Supporting our Police is vital.
"Labour support the law breakers who have disrupted the lives and businesses of Londoners. They cannot be trusted in Downing Street or the Home Office."
Meanwhile other well-known figures have spoken out against the ban.
Shadow home secretary Diane Abbott said: "This ban is completely contrary to Britain's long-held traditions of policing by consent, freedom of speech, and the right to protest."
Teenage climate activist Greta Thunberg tweeted: "If standing up against the climate and ecological breakdown and for humanity is against the rules then the rules must be broken."