Toyota said in a statement it would restart domestic production at its 14 domestic factories from Wednesday. The suspension on Tuesday was seen hitting output of around 13,000 vehicles.
Supplier Kojima Industries Corp, which provides plastic parts and electronic components to Toyota, said in a separate statement that it discovered an error at one of its file servers on Saturday night. After rebooting the server, it confirmed it had been infected with a virus, and found a threatening message.
A Kojima spokesperson said the message was written in English, but declined to give further details.
No information was available about who was behind the attack, nor the motive. It came just after Japan joined Western allies in clamping down on Russia after it invaded Ukraine, although it was unclear whether the attack was related.
Kojima said it was in contact with authorities.
The incident at the Toyota supplier exposes a potential weakness for Japanese industry. While big companies have cyber security measures in place, the government is worried about small or mid-level subcontractors, the industry minister, Koichi Hagiuda, told reporters on Tuesday.
Toyota shares were flat by midday in Tokyo, while the broader market was up 1.5%.