They were arrested in two batches -- 20 on July 5 and 21 on August 30 -- for allegedly entering Lankan waters.
Their remand had been extended by a court at Mannar in Sri Lanka till September 25.
The fishermen said they had withdrawn the protest as they expected the fishermen to be released on September 25. Besides the festival season was also coming,they said.
Fishermen had launched their protest on September 6 voicing concern over continued incarceration of their colleagues in Lankan jails and demanded immediate steps by the Centre to set them free.