Boris Johnson has thrown the Southbank Centre's £120m redevelopment plans into disarray by declaring that a part of the complex used by skateboarders should be left unchanged.

The surprise intervention could threaten the whole scheme as the centre planned to use the undercroft that has been used for decades by young skaters as retail units to generate income.

Johnson told a preliminary planning meeting at City Hall, London, that he supported much of the Southbank Centre's plans, but not moving the skaters from their present home.

He said: "I wholeheartedly support the principle of enhancing the world-class cultural facilities at the Southbank Centre and am encouraged by many of the aspects of their plans. However, redevelopment should not be at the detriment of the skate park, which should be retained in its current position.

"The skate park is the epicentre of UK skateboarding and is part of the cultural fabric of London. This much-loved community space has been used by thousands of young people over the years. It attracts tourists from across the world and undoubtedly adds to the vibrancy of the area – it helps to make London the great city it is."

Johnson's decision now threatens to derail the entire project. In a statement the Southbank Centre said: "We are surprised by the mayor's unexpected statement. We look forward to hearing how he intends to fill the financial gap that now stands between us and our ability to provide free art and culture to millions of Londoners. In the meantime the Southbank Centre board must consider the implications for the future of the project if he fails to do so."

The Southbank Centre wants to create a new Festival Wing, redeveloping the brutalist 1960s buildings that include the Hayward Gallery, the Queen Elizabeth Hall and the Purcell Room. Its most visually eye-catching proposal is for a spectacular glass pavilion that would "float" above the complex, providing space for orchestras and choirs to rehearse.

Johnson said he backed the glass pavilion idea, but he was not in favour of the proposal to move the skaters 120 metres upriver to a new space under the Hungerford Bridge.

The mayor's intervention appears to be a serious setback for the Southbank Centre, with the proposals already opposed by its neighbour the National Theatre.

The National's director Nicholas Hytner wrote a long letter of objection to Lambeth council last summer in which he said "irreparable harm" would be done to the setting of the NT's buildings, threatening a "signature night-time view of London".

Attempting to move the skaters was never going to be easy. They have been there since 1976, and this month the Long Live Southbank campaign delivered a 27,286-name petition to the council objecting to the move.

The Southbank Centre enlisted Søren Nordal Enevoldsen, considered one of the world's top architects for designing skateboarding and urban arts spaces, to come up with plans for a new space under the Hungerford Bridge.

Lambeth council has yet to decide on the planning application, but the mayor's office said it would be referred back to the mayor in any event, making Johnson's position key.