The jellyfish were found obstructing cooling water filters on Tuesday.
The East Lothian plant's operator, EDF Energy, said the shutdown was a precautionary measure and there was never any danger to the public.
A clean-up operation is under way, but it is understood it could be next week before Torness is operational again.
Torness has two Advanced Gas Cooled Reactors but also relies on supplies of sea water to ensure it operates safely.
It has filters which are designed to prevent seaweed and marine animals entering the cooling system.
Continue reading the main storyThere are no radiological aspects associated with this event and there has been no impact to the environment”End Quote EDF spokesman If these screens become clogged, the reactors are shut down to comply with safety procedures.
An EDF spokesman told BBC Scotland: "At no time was there any danger to the public. There are no radiological aspects associated with this event and there has been no impact to the environment."
Staff at the plant took the decision to shut down the reactors on Tuesday afternoon.
It is not known why there are so many jellyfish in the area.
Water temperatures along the east coast of Scotland have been relatively normal, but it is thought higher than average temperatures elsewhere in the North Sea may be a factor.
Operations at nuclear power plants in Japan have been disrupted by large numbers of jellyfish in recent years.
Earlier this month, an Atlantic Grey Seal was rescued from EDF Energy's Hinkley Point nuclear power station in Somerset after it got trapped in the inflow area chasing fish. The plant's operations were not affected.
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