London Mayor Boris Johnson has intervened in a row over the sponsorship of a major cable car project which appeared to discriminate against Israel.

Mr Johnson ordered Transport for London commissioner Sir Peter Hendy and the Emirates airline to remove a clause in the contract for the Emirates Air Line, as the cable car crossing the Thames in east London is known.

It was thought that the agreement with Emirates could have been used to stop TfL doing financial deals concerning the cable car with Israeli banks and companies.

Mr Johnson said he had been unaware of the deal’s details until they were revealed on Tuesday following a Freedom of Information request from the MayorWatch website.

Following Sir Peter’s discussions, the Mayor’s spokesman said: “Emirates agreed to remove the clause and rework the wording. The Mayor is pleased Emirates has moved quickly to clarify the situation.”

Details of the agreement showed TfL had agreed to abide by United Arab Emirates rules on having no ties to “conflicting persons” with which the country will not work. The UAE has no diplomatic relations with Israel.

The UK Lawyers for Israel group had warned that the deal could breach discrimination legislation.

Amir Ofek, spokesman at the Israeli embassy in London, said the arrangment raised “serious concerns”.

A section of the sponsorship contract — worth £36 million over 10 years — made reference to “conflicting persons”, described as any “competitor” of Emirates, or “any person who is a national of, or who is registered, incorporated, established or whose principal place of business is in a country with which the United Arab Emirates does not… maintain diplomatic relations”.

A TfL spokeswoman had initially attempted to laugh off concerns that the deal would preclude Israeli companies from undertaking work linked to the £63m project, or that Israelis could effectively be banned from travelling on the system.

The spokeswoman claimed: “Some people have read too much into it”.

Following the removal of the clause on Tuesday, TfL’s Danny Price, head of the cable car project, said: “The intention behind it was always to give Emirates the option to withdraw their sponsorship should we sell the Emirates Air Line to someone else, something which is common in such contracts.

“We will work on, and publish, alternative wording to express this in these simple terms.”

An Emirates spokeswoman said the clause had been “misinterpreted”.

“It was put in place to protect the commercial interests of the Emirates brand. The clause was not intended to discriminate against any particular person, religion or country. Emirates does not discriminate against passengers of any race, people or religion,” she said.

The cable car connects the Docklands area on the north bank of the Thames with Greenwich on the south bank. It opened in June last year and receives further funding from the Greater London Authority, acting on behalf of the Department for Communities and Local Government.

The revelations raise questions over sponsorship deals signed with Emirates by other organisations, including Arsenal FC, Durham County Cricket Club, and tennis’ ATP World Tour. London Assembly member Andrew Dismore has written to the chief executives of a dozen companies and organisations which have deals with the UAE firm asking whether the deals include similar clauses.