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Nasa officials insist that the other two fuel cells are working normally and that the spacecraft and its crew of five men and two women are in no danger.
But after a day of intensive discussion, the decision was taken to bring Columbia back early, with touchdown at 1434 local time (1834 GMT) today.
The shuttle had been in orbit for just four days, out of a mission planned to last over two weeks.
Tommy Holloway, manager of the US space shuttle programme, told a news conference the fault in the fuel cell meant the supercold liquid hydrogen and oxygen it uses to generate electricity might overheat and mix, causing a disastrous explosion.
"We have come to the conclusion that the conservative thing to do is to land the shuttle," he said. "We have learnt always to be conservative in issues of research."
There are three electricity generating units on board Columbia, providing the power to conduct planned experiments and also to make drinking water for the crew.
Each of them is made up of 96 cells, arranged in three 32-cell "substacks".
Almost immediately after lift-off on Friday, engineers noticed lower than expected power from one of the substacks in unit two.
Safety 'might be jeopardised'
The unit continued to weaken during the next 18 hours of the flight. It was feared that allowing it to continue deteriorating would seriously jeopardise the safety of those aboard.
Nasa is still haunted by the Challenger disaster more than 10 years ago, when the space shuttle exploded just after lift-off. All seven crew members died.
The Columbia crew was to have carried out an ambitious program of research. It included lighting controlled fires in space to see the effect of zero gravity on flame.
The shuttle also carried a greenhouse unit for plants to study the effect of weightlessness on growth.
The Columbia space shuttle is the oldest of the four shuttles in the fleet.
It has had problems with fuel cells before, causing an earlier mission in 1981 - only the second Nasa shuttle mission - to be cut short.
There has been only one other aborted shuttle mission, in 1991, when a navigation device developed a fault.
The aborted flight was relaunched on 1 July 1997 with the same crew of seven on board Columbia. This time the mission was carried out in full, landing on 17 July without mishap.
Columbia continued carrying out shuttle missions without a problem until February 2003, when disaster struck.
Right at the end of a routine mission, just as it re-entered the Earth's atmosphere 16 minutes before its scheduled landing, Columbia disintegrated, killing all seven astronauts on board.
An independent investigation confirmed initial suspicions that a piece of insulating foam from an external fuel tank which hit the shuttle's left wing as it took off was to blame.
The foam had damaged the shuttle's heat shield, causing it to break up on re-entry.
Shuttle flights have since been suspended. Nasa has set a target date to resume shuttle missions in May 2005, with stringent new safety procedures in place.
Discussions continue over how to replace the ageing fleet of space shuttles when they reach the end of their original design life in 2010.
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