The ministry said the Taiwanese-flagged boat was heading toward the Somali coast at full speed when it lost contact with a fishing company early Friday, the Taipei Times reported.
The boat was suspected to have been seized by Somali pirates at 2 a.m. near the Seychelles Islands about 600 miles off the southeast coast of Mogadishu, the ministry said in a release.
The Somalia Report Web site cited maritime sources saying the boat had been seized 260 nautical miles southwest of the Seychelles.
Those on board included a Chinese captain and Vietnamese, Indonesian and Filipino passengers.
The Times said the incident has been reported to the Piracy Reporting Center at the International Maritime Organization's International Maritime Bureau in Kuala Lumpur, Malaysia.
The ministry said it has instructed its missions in South Africa, the United Kingdom, the United States, France, the European Union and Dubai to request those governments help rescue the ship.
Help has also been sought from the U.K. Maritime Trade Organization and other groups, the ministry said.