The five agreements to be signed also include pharmaceutical codes, railway cooperation and maritime and airborne search and rescue.
"They will certainly further broaden and consolidate the ties with Japan," foreign ministry spokeswoman Anna Kao told AFP today.
The Japanese filed more than 10,000 patent applications with Taiwanese authorities each year, compared with around 3,000 patent applications Taiwan sought with Japan, government figures showed.
But Kao would not comment on local media reports which saw the accords as a prelude to a tax and economic cooperation agreement.
Taiwanese government officials hailed the fishing pact as a milestone in ties with Tokyo, although Beijing voiced concerns over the deal with Taiwan, which it still considers part of its territory.
Talks over fishing rights started in 1996 but were suspended in 2009, before being resumed in November last year.
Under the agreement, Taiwanese fishermen will be able to operate in an overlapping 200-nautical-mile exclusive economic zone claimed by Taipei, Tokyo and Beijing.
The waters around the islands are considered potentially rich in natural resources, and Taiwanese fishermen claim ancestral fishing rights.
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