Toyota's body-making subsidiaries in the quake zone, Kanto Auto Works Ltd. and Central Motors Co., will also keep plants closed.
The shuttered plants account for about 45 percent of Toyota's global production.
Toyota will decide when to restart production after reassessing damage and the condition of its supply chain on Monday, spokesman Keisuke Kirimoto said.
"It's first things first. And that's safety," Kirimoto said.
Toyota was still trying to get a grip on damage at plants in the disaster area, he added.
No Toyota employees were injured when the deadly March 11 tremblor struck off Japan's northeast Pacific coast.
Authorities were still trying to reach towns wiped out by tsunamis or blocked off by impassable roads.
But the death toll was expected to exceed the figure of 1,800 cited in media accounts. Nearly 10,000 people are unaccounted for in the port town of Minamisanriku alone, news reports say.
Toyota was suspending operations partly so employees could regroup with relatives. Many people have gone missing and phone service in the disaster area is almost nonexistent.
Toyota had planned to produce 3.89 million vehicles in Japan this calendar year, including output from its Hino truck-making and Daihatsu minicar subsidiaries. That's down 4 percent from 2010, but still represents nearly half of its global production forecast of 8.69 million vehicles.
Automakers are also concerned about damage to plants and the possibility of aftershocks. In addition, they have to ensure that suppliers are intact and ready to keep delivering parts.
A new concern was the possibility of a meltdown at a nuclear power plant damaged by the quake and tsunami. Authorities are rushing to prevent that but have expanded the evacuation zone to a 12 mile radius around the site. Small amounts of radiation are already leaking, reports say.
The killer 8.9-magnitude earthquake and the tsunami waves it triggered ruptured gas lines, wiped out villages, devastated ports and turned coastal areas into swampy morasses.
Aftershocks, many strong, continued rocking the region through Sunday.
Fuji Heavy Industries Ltd., the maker of Subaru cars, closed five factories after the quake. It was unclear if it would resume operations on Monday.
Automakers including Mazda and Suzuki were largely spared from the quake's effects initially because they have assembly plants in other areas of the country.
But the companies are still gathering information about the impact on suppliers and distribution systems.
Mitsubishi had intended to resume work on Monday. But a spokesman said Sunday that its assembly plants would rest through Tuesday while the company coordinated parts shipments and distribution with suppliers, some of whom are in the quake zone.