All shipments of fresh and frozen fruits, vegetables, marine and milk products, as well as mineral water from Japan will be checked, said Hsiao Mei-ling, deputy chief of the Department of Health.
Until Monday's announcement only random checks had been carried out, she said.
The tightened checks will also be imposed on processed food items such as instant noodles, chocolate, rice crackers, and biscuits manufactured in Japan after the killer quake, she said.
The move comes after Taiwanese authorities discovered radiation particles on 14 kilograms (38 pounds) of fava beans from Kagoshima.
It was the first report of polluted food being found outside Japan since the crisis at a nuclear power plant triggered by a devastating earthquake and tsunami 10 days ago.