Plutonium has also been found in soil at the plant, but not at levels that threaten human health, officials say.
Earlier, Japan's government strongly criticised the plant's operator, Tepco, over mistaken radiation readings.
Tepco announced on Sunday that a highly radioactive pool of water in the No 2 reactor was 100 times more radioactive than it actually was.
Officials said the radiation scare was caused by a partial meltdown of fuel rods.
Underground tunnel The discovery of highly radioactive water outside a reactor building is a worrying development, says the BBC's Mark Worthington in Tokyo.
Up until now, pools of water with extremely high levels of radiation have only been detected within the reactor buildings themselves.
FUKUSHIMA UPDATE (28 MAR)
- Reactor 1: Damage to the core from cooling problems. Building holed by gas explosion. Highly radioactive water detected in reactor
- Reactor 2: Damage to the core from cooling problems. Building holed by gas blast; containment damage suspected. Highly radioactive water detected in reactor and adjoining tunnel
- Reactor 3: Damage to the core from cooling problems. Building holed by gas blast; containment damage possible. Spent fuel pond partly refilled with water after running low. Highly radioactive water detected in reactor
- Reactor 4: Reactor shut down prior to quake. Fires and explosion in spent fuel pond; water level partly restored
- Reactors 5 & 6: Reactors shut down. Temperature of spent fuel pools now lowered after rising high
The water was found in an underground maintenance tunnel, with one end located about 55m (180ft) from the shore.
Radiation levels were measured at 1,000 millisieverts an hour, a dose that can cause temporary radiation sickness. This is the same as the levels found on Sunday. However, Tepco said there was no evidence that the contaminated water had reached the sea.
Tepco later said that plutonium had also been detected in soil at five locations at the plant but not at levels that represented a risk to human health.
It said the results came from samples taken a week ago and would not stop work at the plant.
Plutonium was used in the fuel mix for only one of the six reactors, number three.
The twin discoveries came hours after the government criticised Tepco for issuing incorrect readings from the plant.
On Sunday Tepco said radiation levels at reactor No 2 were 10 million times higher than normal before correcting that figure to 100,000.
"Considering the fact that the monitoring of radioactivity is a major condition to ensure safety, this kind of mistake is absolutely unacceptable," said Chief Cabinet Secretary Yukio Edano.
Tepco has apologised but the mistaken reading at the Fukushima Daiichi plant has called into question the operating company's handling of the current crisis, our correspondent says.
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