The Nuclear and Industrial Safety Agency's excuse is that the operator, Japan Atomic Energy Agency, did make an announcement of the trouble "locally" - probably meaning the municipality where the fast breeder is located.
From Yomiuri Shinbun (1/20/2012):
Trouble at Monju, cause unknown. May further spur the debate whether to continue the project
The Nuclear and Industrial Safety Agency under the Ministry of Economy, Trade and Industry instructed the Japan Atomic Energy Agency (JAEA) to investigate the cause of malfunction at the driving mechanisms for the control rods at the JAEA's fastbreeder "Monju" (in Tsuruga City, Fukui Prefecture), and to come up with measures to prevent it from happening again.
According to NISA, the malfunction happened on December 12. Of the 19 driving mechanisms for the control rods, one mechanism didn't work at all when they conducted the test to verify the mechanisms were working. When tested again 2 days later, the mechanism worked. However, there is another mechanism that didn't work [and didn't work in the 2nd test]. JAEA says they will disassemble the mechanism in order to identify the cause.
As to why the disclosure was so late, NISA explained that the control rods were all in, and JAEA did announce locally. The control rods are all inserted, and the Monju reactor is safe at this time. However, the government has been reviewing its nuclear policies in the aftermath of the Fukushima I Nuclear Power Plant accident, including whether to continue the Monju project. The trouble this time may spur the debate.
Not just the malfunction trouble, but the fact that the regulatory agency NISA felt it was OK to wait for more than one month to announce the problem should raise alarm.
NISA's press release on January 20 states that JAEA must report back to the Agency by February 29.