An extra £18.6 million is needed to repair the tower which houses Big Ben, parliamentary authorities have been told.
The new costs would see the renovation bill rise by almost a third from £61.1 million to £79.7 million - the original estimate for the project was forecast at £29 million.
The increase has been put down to the discovery of asbestos, pollution and the discovery of extensive Second World War bomb damage in the Elizabeth Tower - home to the capital’s famous bell.
The programme of works on the 160-year-old tower began in 2017 is expected to complete by 2021.
A spokesman for the House of Commons Commission said members were "extremely disappointed" by the request for "yet more funding".
"It is very frustrating to learn that the Elizabeth Tower project requires yet more funding, having agreed an extra £32 million in 2017," he said.
"We have requested more detailed information about the lessons learned from this experience – as well as assurances that more robust estimates are prepared for works of this nature in the future."
The full scale of the work needed to complete the refurbishment by the late 2021 deadline only became clear when the renovation team began the first ever "intrusive surveys" on the 177-year-old structure, officials said.
The latest setback discoveries included the discovery of asbestos in the belfry, broken glass in the clock dials, extensive use of toxic lead paint and defects in previous work.
Ian Ailles, director general of the House of Commons, said the works are proving "more complex than we could have anticipated".
"With a 12m square (130 square feet) footprint and a prime location right in the middle of a busy working Parliament, understanding the full extent of the damage to the Tower was impossible until the scaffolding was up," he said.
He added: "Alongside other issues, such as the impact of often inappropriate conservation methods used by our predecessors, the corrosive levels of pollution in the atmosphere and the discovery of asbestos in unexpected places, we have only now been able to fully understand the full investment required for this project."
The new budget will be set if it is approved by the accounting officers of the two houses.