Lee told reporters that the Taiwan-Japan dialogue mechanism on maritime affairs cooperation that is expected to be launched by the end of July will be broader in scope than the existing bilateral fishery committee.
Besides fishery cooperation, he said, the dialogue will also cover issues such as maritime emergencies and rescue.
He said the two sides have discussed the matter for quite some time and that Japan has been very sincere.
The minister said he is very optimistic and confident that the mechanism will better protect the rights and interests of Taiwanese fishermen.
Also Tuesday, Presidential Office spokesman Alex Huang said that because the fishery dispute between Taiwan and Japan over the Okinotori atoll remains unresolved, there is a need for continued negotiations to uphold the rights of Taiwanese fishermen in the area.
He said that replacing confrontation and conflict with dialogue and cooperation is the government's principle in dealing with international affairs and that the Presidential Office looks forward to the opening of Taiwan-Japan dialogue on maritime affairs.
The Okinotori dispute erupted after a Taiwanese fishing boat was detained by Japan April 25 on the high seas near the Japan-controlled atoll.
The administration of former president Ma Ying-jeou lodged a strong protest with Japan after the Japanese authorities refused to release the boat until the owner had paid a security deposit of 6 million Japanese yen (about US$54,000).
Japan claims that the atoll is an island and that it is therefore entitled to a 200-nautical-mile exclusive economic zone. But Taiwan insists that it is not an island because it cannot sustain human habitation, and accused Japan of using land reclamation to expand the atoll.
Ma has previously proposed submitting the dispute to international mediation and arbitration.