The agreement allows Taiwan to fish within 19km (12 miles) of the islands, known as Senkaku in Japan and Diaoyu in China.
China and Taiwan both claim the island chain, which is controlled by Japan.
China claims sovereignty over Taiwan, which does not have official diplomatic relations with Japan.
The deal comes after 17 years of negotiations between Japan and Taiwan, local media has reported.
The islands offer rich fishing grounds and are thought to contain oil deposits.
They have been at the heart of considerable diplomatic tension between China and Japan, most recently in January when Japan said a Chinese frigate put a radar lock on a Japanese navy ship near the islands - something China disputes.
In January, a boat of Taiwanese activists also tried to reach the islands, but were forced back by the Japanese coastguard.
'Special partnerships'
"These negotiations are about the protection of maritime resources in the East China Sea," Japan's Chief Cabinet Secretary Yoshihide Suga said on Wednesday.
He added that the deal had no relation to the territorial dispute. "The Senkaku islands are inherently our national territory. Therefore there are no issues being shelved here."
Liao Liou-yi, Chairman of Taiwan's Association of East Asia Relations, said that relations on both sides were at the "highest positive level" and that Taiwan and Japan had "special partnerships".
Many analysts believe that Japan agreed to the deal to prevent China and Taiwan from presenting a united front against it over any territorial dispute.
China has expressed opposition to the agreement. It claims sovereignty over Taiwan, and insists that nations cannot have official relations with both China and Taiwan.
"China's position on Taiwan's foreign exchanges is clear and consistent," Chinese Foreign Ministry spokesman Hong Lei said on Wednesday.
"We are extremely concerned about Japan and Taiwan discussing and signing a fishing agreement."-British Broadcasting Corporation (April 10, 2013)
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