The issue was discovered on Wednesday during routine maintenance at the facility, near Dunbar in East Lothian.
Operator EDF Energy said the manual shutdown was carried out as a precaution with no safety, health or environmental impacts.
Reactor one is still generating electricity and EDF expects reactor two to be back online soon.
Station director Paul Winkle said: “Whilst carrying out routine maintenance in the conventional turbine part of the plant, there was an issue with a valve and our operations team took prompt action and manually shut down the reactor, putting safety first.
“Cooling to the reactor was maintained at all times and there were no safety, health or environmental impacts.
“The reactor will be returned to power as soon as maintenance is satisfactorily completed.”
In February it was announced that Torness nuclear power station will have its life extended by seven years, remaining operational until 2030.
The power station started operating in 1988 and now employs 550 full-time staff plus around 180 contractors.
Its two nuclear reactors generate enough electricity to power more than two million homes, according to the French firm.