Quarantine fees shall be charged for 0.1% of the Free on Board (FOB) value of the export articles or the import duty value for the imported articles. Quarantine fees shall be charged at the rate of 0.05% of the import duty value of the imported articles which are wheal, barley, corn or soy bean.

For export purposes, the fee for certain animal diseases and plant pests sampling test shall be charged as follows. The fee for specific animal diseases test for urgent exportation shall be doubled.
1. A fee of NT$ 1,000 for the enzyme-linked immunosorbent assay (ELISA).
2. A fee of NT$ 1,600 for Polymerase Chain Reaction (PCR).
3. A fee of NT$ 2,100 for Reverse Transcription PCR (RT- PCR).
4. A fee of NT$ 3,100 for Real Time RT-PCR.
5. A fee of NT$ 3,600 for virus isolation.

Exporters, importers (hereinafter referred to as “the applicants”) or the agents, when applying for inspection, shall submit the foreign currency exchange documents or other sales documents in order to calculate the quarantine fees. If such documents are not available along with the inspection application, it is required to submit before issuing the phytosanitary/veterinary certificates. For those merchant groups or associations, where approval is granted by the competent authority to calculate the fees based on uniform values, submission of the aforementioned documents will be exempted.

For those articles exempt from acquiring import or export permits, quarantine fees are charged as follows:
1. Fees for the import articles are charged for the import customs declaration form signed by the declarant, or foreign exchange documents such as the trade invoice from overseas exporters, submitted by the applicants or the agents while applying for inspection.
2. Fees for the export articles are charged for the letter of credit or export customs declaration form signed by the declarant submitted by the applicants or the agents while applying for inspection. However, the fees shall be charged as per local sales invoices, commercial invoices or other sales proof documents, when application is submitted at local manufactory.

The quarantine fees shall be exempted for the following cases:
1. The articles are used for military purposes and accompanied with proof from military authorities.
2. The articles of imported food are used for military or official purposes and accompanied with proof from food administration authorities.
3. The allowed quantity of quarantine objects or regulated articles carried by passenger or crew serving on vehicles, vessels and aircrafts pursuant to the Regulations for Quarantine of Animal/Plant Regulated Articles Carried by Passengers and Service Personnel on Vehicles or the Regulations for Quarantine of Plant Regulated Articles Export and Import by Mail.
4. Unprocessed raw, cold-stored or frozen livestock or poultry meat for export, where the meat inspection fee has been paid for at slaughtering.

For the export articles paid with foreign currencies, the quarantine fees shall be charged as per the payment which should be converted into NT$, based on the exchange rates applicable for custom declaration as stipulated by the directorate general of customs for every ten-day period.