According to an emergency email from Nuclear Regulatory Authority that independent journalist Ryuichi Kino shares, the cause of the system stoppage is not likely to be known anytime soon as the maintenance staff cannot reach Monju because of landslides caused by Typhoon 18's heavy rain.
From Kino's tweets:
Today (September 16), we at Nuclear Regulatory Authority received correspondence from Japan Nuclear Energy Safety Organization (JNES) that data transfer from the plant parameter display system of the Emergency Response Support System (ERSS) for Japan Atomic Energy Agency (JAEA)'s Monju Fast-Breeder stopped.
(The data transfer stopped at 2:56AM on September 16, and partially resumed after 3:46AM.) JNES and JAEA are currently investigating the cause of the data transfer stoppage. However, because of landslides from heavy rain from Typhoon No.18, maintenance and repair staff cannot get to the Monju Plant compound. Therefore, it may take a while to determine the cause of the stoppage.
We have already instructed JAEA to secure the collection and transfer of data via alternative means such as telephone, FAX, email if a problem arises at the nuclear facility before the ERSS data transfer system is fully restored.
According to Asahi Shinbun (9/16/2013), there were two landslides near Monju, with one of them at the entrance of a tunnel 1 kilometer from the plant.
There are several nuclear power plants in Japan which are only accessible by one road and/or a tunnel - Monju, Tsuruga Nuclear Power Plant, and Ooi Nuclear Power Plant.
Here's how Monju is situated: accessible via a tunnel, or a narrow road hugging the coastline:
Accessibility to the site in case of a problem is not included in the conditions for restarting the nuclear power plants in Japan.
By the way, in terms of accessibility, TEPCO's nuclear plants including Fukushima I Nuclear Power Plants are one of the best nuclear plants in Japan, and still the earthquake and tsunami led to the disaster we continue to face at Fukushima I Nuclear Power Plant.