There were severe delays on the Jubilee line on Saturday as the long overdue new signalling system was used in public service for the first time.
London Underground says that the new system – which should have been in operation last year – will increase the line's capacity and reduce journey times.
Jubilee line passengers have endured weekend after weekend of closures for the installation and testing of the new system.
In June Transport for London brought responsibility for the upgrade in house when it acquired Tube Lines, the former public-private partnership infrastructure company.
A paper presented to the TfL board last month set out a catalogue of faults and glitches revealed by non-public tests of the new signalling.
Now LU says that there is only a "slim chance" of completion by the end of 2010.
The signalling system was used in public service for the first time on Saturday between Waterloo and Stratford but by 8am the service had been suspended due to a signal failure.
Delays persisted throughout the day and a hand-written notice on the whiteboard at Southwark Station warned passengers that they faced waits of 15-20 minutes to catch a train and advised them to use alternative routes.
"It is now clear that we inherited from Tube Lines a Jubilee line upgrade programme which was badly behind schedule," says LU managing director Mike Brown.
"When complete it will mean great improvements for passengers – with capacity boosted and journey times reduced, and we are now taking a major step forward by using the new signalling for the first time in passenger service.
"I would like to apologise to passengers, communities, and businesses who have suffered years of closures. Although there is only a slim chance of completion by the end of the year, we are doing everything possible to get the job done as soon as possible, whilst keeping disruption to an absolute minimum."
To enable the full end-to-end system to be tested, the whole Jubilee line will need to close for one weekend in October, one in November, and over the Christmas period.
"This is grim news for all the Jubilee line passengers who have suffered so much disruption over months and years," said Caroline Pidgeon, leader of the Liberal Democrat London Assembly group.
"There is no light at the end of the tunnel: just more and more closures.
"The upgrade of the Jubilee line is demonstrating exactly how not to upgrade the tube. There is now overwhelming evidence that blockades of short sections of the tube for two or three weeks would be a far better way to upgrade the tube than the fiasco of literally years and years of weekend closures."