The Tube's efficiency and reliability are embarrassing, if not disgraceful, and must change, London Transport Commissioner Bob Kiley has said.
Bob Kiley said similar delays had happened 'scores of times'
The criticism comes after thousands of commuters faced rush hour delays on four main Tube lines on Wednesday.
Mr Kiley told the London Assembly the performance of Metronet, part of the public-private partnership deal (PPP), was "completely unacceptable".
Metronet said repair work was now on track but would take time.
Morning delays on the District, Metropolitan, Bakerloo and Northern Lines were due to overrunning works at Whitechapel, east London.
Metronet and Tube Lines are the two consortia responsible for the maintenance and upgrading of the underground because of PPP.
The companies' contracts run for 30 years, although there is a clause for renegotiation in 2010.
Mr Kiley told assembly members at City Hall: "The rush hour for half of the city was a disaster this morning.
"That has happened scores of times during the short lives of these contracts - I find that to be completely unacceptable.
"We get efficiency and reliability out of our rail system both overground and underground that are embarrassing, if not downright disgraceful and that definitely has to change."
The outburst is being seen by some as an indication Mayor Ken Livingstone may try to dismantle PPP.
BBC London News political editor Tim Donovan said: "The Mayor always said after two years he would go to the government if PPP was demonstrably not working.
"Now Bob Kiley is saying it's not working."
A spokesman for Metronet said more potential faults were discovered early because of advanced technology meaning a safer Tube for all.
"Whilst there have been some start-up delays to our massive capital programme, work is now advanced on new track, new station improvements, new trains and new signalling."