The meeting will aim to smooth over differences in fishing procedures in a designated area of the East China Sea, where Taiwanese and Japanese fishermen are allowed to operate freely, according to Lo Koon-tsan, secretary-general of the association.
The meeting will be held at GIS NTU Convention Center at Taipei's National Taiwan University and could run into Friday if necessary, said the Interchange Association, which represents Japan's interests in Taiwan, reports WantChinaTimes.
Officials from both countries' foreign ministries, fisheries agencies and maritime law enforcement are set to attend.
The first meeting of the fishing commission took place in May 2013 in Taipei, while the second was held in December, in Tokyo.
At the second meeting, the countries remained divided on fishing operations in their overlapping waters in the East China Sea, but agreed to continue negotiating on the issue, according to Taiwan's Ministry of Foreign Affairs.
The Tokyo talks came after fishermen's associations from Taiwan and Japan met in Yilan County, northeastern Taiwan, for talks earlier in the month about the differences in their fishing methods.
One sticking point of that meeting involved the direction in which fishing lines are deployed and the distance maintained between longline fishing boats when they are operating in the overlapping exclusive economic zones.
Japanese fishermen advocated their operating method, which requires fishing boats to set their lines in a north-south direction and maintain a distance of 4 nautical mile between each boat.
Taiwanese fishermen, however, who are more numerous in the area, said they would stick to their traditional approach of deploying lines in an east-west direction and maintaining a distance of 1 nautical mile between boats.
The Taiwan-Japan fishing commission was established as part of an agreement signed April 10, 2013 by the two countries on fishing rights in the East China Sea near the disputed Diaoyutai islands, known as the Senkaku islands in Japan, and also claimed as the Diaoyu islands in China.
Under the terms of the April agreement, Taiwanese and Japanese boats can operate freely in a 74,300 square kilometer area around the uninhabited islets, Taiwan's Fisheries Agency said.