TOKYO — The damage to one of three stricken reactors at the Fukushima Daiichi plant could be worse than previously thought, a recent internal investigation has shown, raising new concerns over the plant’s stability and complicating the post-disaster cleanup.

The government has said that the plant’s three badly damaged reactors have been in a relatively stable state, called a cold shutdown, for months, and officials say that continues. But new tests suggest that the plant — which was ravaged last March when a powerful earthquake and tsunami hit the area — might not be as stable as the government or the operator of the plant, Tokyo Electric Power Company, or Tepco, had hoped.

The key to keeping the reactors stable is keeping their fuel rods cool with water.

The company announced this week that an examination of one reactor, No. 2, showed that the water level in an outer containment vessel was far lower than estimated, which could indicate that the already badly damaged uranium fuel might not be completely submerged and, therefore, is in danger of heating up.

Cooling water in that vessel, called the drywell, was just two feet deep, rather than the 33-foot level estimated by Tepco officials when the government declared the plant stable in December. That is probably not a problem for the fuel that the company says has leaked into the drywell from an inner containment vessel because Tepco says that melted fuel is unlikely to be higher than two feet.