TOKYO (Reuters) - Officials from Japan's transport ministry launched an on-site investigation at Toyota Motor's ( TM ) headquarters on Tuesday after irregularities were found in its applications to certify certain models.

The widening fallout over vehicle certification tests stem from a safety test scandal at Toyota's ( TM ) Daihatsu compact car unit and has spread to other Japanese automakers.

But Toyota ( TM ), which has long prided itself on its reputation for safety and reliability, was the only automaker to undergo an on-site inspection.

Japan's transport ministry had announced plans to carry out the inspection a day earlier, when it said Toyota ( TM ), Mazda ( MZDAF ), Honda ( HMC ), Suzuki and Yamaha Motor ( YAMHF ) were found to have submitted either flawed or manipulated data when applying for certification of vehicles.

Toyota ( TM ) chairman Akio Toyoda, the grandson of the automaker's founder, apologised to shareholders, car fans and other stakeholders at a press conference on Monday.

"From a compliance standpoint, we think further strengthening of governance will be needed going forward," analysts at Goldman Sachs wrote in a note to clients.

Toyota's ( TM ) shares were down 1.1% on Tuesday morning, extending Monday's 1.8% loss. Those of Honda ( HMC ) dropped 2.3%. Suzuki's and Mazda's ( MZDAF ) shares both rose 0.9%.

Toyota ( TM ) and Mazda ( MZDAF ) said on Monday they had both halted shipments of some models.