The COA intensified implementation of the "Hog Cholera and Foot and Mouth Disease Eradication Program" in an effort to wipe out these diseases at the earliest possible date. There was no foot and mouth disease case reported in Taiwan after February 2001, and the International Office of Epizootics (OIE) designated Taiwan a "Vaccine-using Foot and Mouth Disease Free Country" on May 22, 2003. To prevent the entry of major pests and diseases from overseas, and thereby protect agricultural production and citizens' health, the COA performs continuous monitoring for rabies, mad cow disease, rinderpest, avian influenza, the Mediterranean fruit fly, the codling moth, and the nematode Globodera rostochiensis. This vigilance has kept Taiwan free of these harmful pests and diseases. Furthermore, the COA has strengthened plant, animal, and their product import and export disease testing and quarantine work at ports of entry and departure. In 2003, 91,193 batches of products were subjected to import quarantine and 53,494 batches were subjected to export quarantine.

As for monitoring heavy metal contamination of crops, the COA destroyed 4,890 kg of rice from five pieces of farmland after it was discovered that cadmium content exceeded standards. The COA tested produce for pesticide residues in the field and at collection depots; 98% of 14,099 random samples passed chemical testing. For drug residues in livestock and poultry, total 89,584 random samples of pork, pig's liver, pig's blood, chicken meat, chicken eggs, duck meat, duck eggs, and raw milk were detected and 99.59% of these samples met standards. In the case of those samples that failed testing, the COA performed investigation and penalty or fine, in accordance with the law, and implemented tracking and assistance to ensure the safety of agricultural products.

The COA supervised the improvement of livestock and poultry slaughterhouse facilities, implemented slaughter sanitation measures, and sent 345 veterinarians to implement slaughter sanitation inspections at slaughterhouses. Sanitation inspectors supervised the slaughter of 8 million and 130 thousand (8,130,000) hogs and other livestock and 168 million and 20 thousand (168,020,000) poultry in 2003. To ensure the sanitation and safety of meat products, the COA intensified its crackdown on illegal slaughter behavior.