Toyota shares fell on Thursday when Japan's Transport Ministry inspected its subsidiary Daihatsu over safety concerns dating back decades and as the world's top-selling automaker later separately announced a recall of some 1.1 million vehicles, mainly in the U.S.

Shares in Japan's biggest automaker closed down 4.0%, underperforming the benchmark Nikkei average, which fell 1.6%.

A day earlier, Toyota's small-car unit, Daihatsu said it would halt shipments of all of its vehicles indefinitely after discovering more safety-inspection irregularities.

An independent committee said it had found issues involving 64 models, including almost two dozen sold under Toyota's brand. The panel had been investigating the unlisted automaker after it said in April that it had rigged side-collision safety tests carried out for 88,000 small cars.

Daihatsu said on Wednesday it did not know when it would resume shipments, but that the impact on its earnings would be substantial.

Analysts said the impact on Toyota's earnings would likely be limited given the parent company's size. A one-month suspension of production, for example, would equal 120,000 vehicles and translate to a revenue reduction of 240 billion yen ($1.68 billion) for Toyota, Nomura auto analyst Masataka Kunugimoto wrote in a report.

A bigger impact could be on Daihatsu's suppliers. The company's supply chain in Japan comprises 8,316 companies that made 2.21 trillion yen in annual sales from Daihatsu, Teikoku Databank said in a report.

Shares in parts manufacturer Metalart, which has strong ties with Daihatsu, plunged 10%.

Daihatsu's infraction drew criticism from the government, with the Transport Ministry saying it would consider administrative penalties including revoking Daihatsu's production certification depending on the outcome of its investigation.

"This is an extremely regrettable case that undermines the trust of automobile users and is a misconduct that affects the very foundation of the automobile certification system," Chief Cabinet Secretary Yoshimasa Hayashi told reporters.

Daihatsu has said it would consider financial support and damages for its suppliers.

Separately, Toyota said it would recall 1.12 million vehicles worldwide, mainly in the United States, to fix a faulty sensor that could cause airbags to not deploy as designed.

Shares in Toyota affiliate and parts supplier Aisin, which manufactured those sensors and is a major supplier for Daihatsu, lost 3.9%.

Shares of Suzuki Motor, Daihatsu's main rival in Japan's mini-vehicle market, rose 2.1%.