By Satoshi Sugiyama

TOKYO (Reuters) -Toyota Motor Corp suspended operations at a dozen assembly plants in Japan on Tuesday due to a malfunction with its production system, the automaker said, likely bringing to a halt almost all of its domestic output.

The automaker was looking into the cause of the problem, a spokesperson said, adding it was "likely not due to a cyberattack". The malfunction has meant the company has not been able to order components, the spokesperson added.

While the exact amount of lost output was unclear, operations were halted at all of Toyota's domestic assembly plants except for two, the Miyata plant in the southern prefecture of Fukuoka and a Kyoto plant run by Toyota unit Daihatsu, the spokesperson said.

All together, its 14 plants in Japan account for around a third of Toyota's global production, according to Reuters calculations. Toyota is the world's largest automaker by sales.

Operations were suspended from Tuesday morning and it was unclear whether they could be resumed from the afternoon shift, the spokesperson said.

Toyota's operations ground to a halt last year when one of its suppliers was hit by a cyberattack. That one-day disruption caused an output loss of around 13,000 cars.

The automaker is a pioneer of the just-in-time inventory management, which keeps down costs but also means that a snarl in the logistics chain can put production at risk.

The outage is the latest blow to corporate Japan. Some Japanese businesses and government offices have reported a flood of harassing phone calls in recent days, which the government has said were likely from China, following the release of treated radioactive water from the Fukushima nuclear power plant into the Pacific.

Shares of Toyota were down 0.3% at 2,429 yen in early Tokyo trade.

(Reporting by Satoshi Sugiyama; additional reporting by Miyoung Kim; Editing by Muralikumar Anantharaman and Christopher Cushing)