Vattenfall says Lars Fagerberg had therefore decided to quit with immediate effect.
The resignation follows much media criticism after a series of safety-related incidents over the past half a year or so, the first being an emergency shutdown of a reactor last July after back-up generators failed to start after a short-circuit.
Reactors at the plant, north of Stockholm, were taken off-line again just last weekend, because of a fault with a rubber seal in an outer wall.
A prosecutor is looking into the July incident and the Swedish Nuclear Power Inspectorate wants UN inspectors to carry out an investigation there.
Sweden’s ten nuclear reactors provide around half of the country’s electricity needs.