Toyota said Monday it had suspended domestic shipments of three car models after falling foul of government certification rules along with its Japanese rivals Honda, Mazda, Suzuki, and Yamaha.

The transport ministry told the companies to stop delivering certain models within Japan after they reported failures to follow standardized steps to certify vehicles for shipment.

On-site inspections will also be carried out, it said.

The latest irregularities came to light after the ministry told 85 automakers and parts suppliers to report breaches related to certification applications -- an edict prompted by a safety test scandal at Toyota subsidiary Daihatsu.

Daihatsu in December admitted manipulating tests since at least 1989 and halted all factory operations, dealing a blow to the Japanese economy.

Its shipments resumed in April after the government lifted a sweeping ban.

"It is extremely regrettable that additional wrongful acts have been revealed," a ministry statement said on Monday.

These "undermine the trust of users and shake the very foundation of the vehicle certification system", it said.

Toyota said it would suspend shipping of the Corolla Fielder, Corolla Axio and Yaris Cross after reporting inadequate data in pedestrian and occupant protection tests.

The world's top-selling automaker said ongoing internal reviews had also found four other models no longer in production were "tested using methods that differed from the government standards".

Toyota's board chair Akio Toyoda apologised to its customers during a press conference but assured them that the vehicles "passed legally set standards." 

Honda said it had found "inappropriate" data entry in tests related to noise and engine power regarding vehicles sold in the past.

But it also stressed that its vehicles were safe and had passed corporate standards, and current models are not affected.

In recent months, Toyota's truck and bus brand Hino has been hit by a scandal over rigged tests of its engines in Japan.

Meanwhile, its affiliate Toyota Industries did not conduct proper output testing for the certification of three diesel engine models.

Toyoda said in January it would "take time to recover the trust back from our customers" and promised to lead a "transformation".