The Garden Bridge Trust says that the project's cost could "substantially exceed" the previously stated £185 million budget for the controversial river crossing.
When Joanna Lumley first proposed a garden bridge across the Thames in 1999 – as a tribute to the late Diana, Princess of Wales – engineers Arup costed the scheme at £19 million.
As recently as 2013 the cost was put at less than £100 million, but last summer the Garden Bridge Trust revised the estimate upwards to £185 million.
£60 million of the scheme's cost is to be met by the taxpayer, with £30 million from Whitehall and £30 million from Transport for London.
In its latest annual report with Companies House, the charity warns that "the final cost could substantially exceed the formal estimate".
Lord Davies, chairman of the Garden Bridge Trust, said: "The Garden Bridge Trust has made significant progress to get to a stage where we have completed detailed pre-construction work and have a contractor on board.
"We have consistently flagged the areas of risk to the project about acquiring land, the signing of the mayoral guarantee, our funding position and the cost of the project. These matters are dependent on third parties and are outside trustees' control and have led to delays.
"The trustees are duty bound to disclose these risks and how we intend to deal with them, in this report. We strongly believe we can progress all outstanding issues and we are determined to make the project happen.
"We look forward to working with our supporters, including the Mayor and the Government to make the Garden Bridge a reality. We expect to start construction in 2017."
Liberal Democrat London Assembly member Caroline Pidgeon AM said: "Even advocates of the Garden Bridge with rose-tinted glasses will find these accounts incredibly concerning.
"The trust has finally admitted what most people have long expected was the case – that the final cost of the project is likely to increase substantially above the current £185 million predicted cost.
"The trust is admitting for the second time that the costs of this project are spiralling upwards. That can only mean an even greater risk to the taxpayer ultimately picking up the costs of this folly of a project.
"The other admissions of the Garden Bridge Trust relating to a wide range of other risks are also significant and should concern every London taxpayer.
"The harsh reality is that the Garden Bridge is on the brink of collapse. The Mayor of London must now do the right thing. He should refuse to provide a taxpayer guarantee for the project and so put the whole sorry saga to an end."
In October last year Mayor of London Sadiq Khan said: "I will not allow any guarantees to be entered into for the maintenance and operation of the bridge unless I am convinced that this will not lead to further public expenditure down the line."
Just before Christmas, Meg Hillier MP, chair of the Public Accounts Committee, warned the Treasury that claims of the Garden Bridge's transport and health benefits "seem entirely tenuous".
The bridge is currently the subject of a value-for-money probe by Dame Margaret Hodge MP, commissioned by Sadiq Khan.
The scheme also faces further scrutiny from Westminster councillors after Labour and Conservative members 'called in' a decision to grant the Garden Bridge Trust rights to build above Temple Underground Station.