The cost of repairing the Elizabeth Tower, which houses the famous Big Ben bell, has risen by £18.6m following the discovery of bomb damage and asbestos.
The need for more money was only discovered during a survey of the 177-year-old structure in central London.
The House of Commons Commission said it was "extremely disappointed" that the cost had risen to £79.7m.
The new budget will have to be approved by the accounting officers of the Houses of Parliament.
Ian Ailles, director general of the House of Commons, said the Elizabeth Tower restoration - which began in 2017 and is scheduled to continue until next year - "had been more complex than we could have anticipated".
He explained that it had not been possible to understand the "full extent of the damage" until scaffolding had gone up and a survey was carried out.
The examination revealed:
- decay and damage to hundreds of intricate carvings
- asbestos in the belfry
- extensive use of toxic lead paint
- broken glass in the clock dials
- the need for a specialist clock expert
The four clock dials on the outside of the tower contain a total of 1,296 individual pieces of glass, each of which need to be replaced as part of the restoration work.
And 700 stone repairs have been needed - 300 more than the initial estimate - and every new piece of stone needs to be painstakingly recarved.
The Elizabeth Tower is often mistakenly called Big Ben by tourists and Londoners alike - but that latter name only refers to the bell that it houses.
The tower only gained its current name, having previously been called the Clock Tower, when it was renamed in honour of the Queen to mark her diamond jubilee in 2012.
A statement from the House of Commons Commission said: "It is very frustrating to learn that the Elizabeth Tower project requires yet more funding, having agreed an extra £32m in 2017.
"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 Elizabeth Tower project is separate from the planned full-scale restoration of the Palace of Westminster.
Both Houses of Parliament are due to temporarily relocate out of the Palace as part of wider refurbishment plans due to begin around 2025.
Plans to put a new Olympics-style delivery body in charge of the works were approved by MPs and peers last year.