TEPCO says the plant's alarm system went off around 10 AM. It showed a rise in radioactivity in the channel that leads to a nearby port.
Measurements showed that levels of beta-ray emitting substances, which are not detected under normal circumstances, had risen to up to 7,230 Becquerels per liter.
The figure is 10 times higher than when rain causes the level to rise temporarily.
The utility suspects that contaminated water in the channel may have leaked into the port.
It has suspended all operations to transfer contaminated water and closed a gate of the channel by the port.
The drainage channel used to be connected to a section of coast beyond the port. TEPCO rerouted it after a series of leaks in 2013.
The company says the water level in a tank that contains contaminated water remains unchanged, showing no signs of leakage, and drain valves that keep water from leaking near the tanks remain closed.
The utility is investigating the cause of the rise of radioactivity in the channel.