The agency said robots would be used to examine the inside of the reactor building as any leakage would interfere with the effort to keep the nuclear fuel inside the reactor pressure vessel cool.
"We are currently examining data, but we think that there is water leakage to some extent," agency spokesman Hidehiko Nishiyama told reporters, Kyodo News reported.
The cooling work involves filling the vessel pressure vessel with water but to do that any leakage must be stopped. Any leakage from the container vessels could cause the submerged fuel to be exposed.
The Wall Street Journal reported the nuclear safety agency spokesman also has leakage concerns about the No. 4 reactor spent fuel pool, which has the most used and active fuel rods among the plant's six reactor buildings.
Most of the Fukushima plant's reactors were damaged by the March 11 earthquake and tsunami which knocked out their cooling systems, requiring workers to keep injecting large quantities of water into the reactor buildings.
However, this process has caused tons of highly radioactive water to collect in the basement of the reactor buildings, which needs to be drained out.
"The robots will examine if there are any leaks and whether the water filling operation can move forward," Nishiyama was quoted as saying. Such robots have been used earlier to measure radiation levels in other reactors.