The fishermen, who hail from Tamil Nadu, will be released ahead of his visit beginning tomorrow, the Prime Minister's Office said in a statement.
It said a fishing organisation in Tamil Nadu had made an appeal to the government to consider the medical condition of the arrested fishermen.
They will be released later today in a "goodwill gesture", the office said.
The veteran reformist, who returned to the office for a fourth term as premier, is expected to hold talks with Prime Minister Narendra Modi, External Affairs Minister Sushma Swaraj and President Pranab Mukhrjee.
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The talks are expected to touch upon the sensitive fishermen issue.
Fishermen from both India and Sri Lanka are often accused of straying into each others' waters and are arrested despite both sides acknowledging the issue to be a 'humanitarian' one.
In March, Sri Lanka ordered the release of 86 Indian fishermen arrested for allegedly poaching in Sri Lankan waters as a goodwill gesture to mark Modi's visit, the first by an Indian premier to this country in over 25 years.
Later the same month, Sri Lankan President Maithripala Sirisena ordered the release of 54 Indian fishermen from Tamil Nadu.
The new unity government in Sri Lanka is reaching out to India and the West to mend ties that soured during Rajapaksa's rule.
In response to opposition criticism that Wickremesinghe was expected to enter the Comprehensive Economic Partnership Agreement (CEPA) with India to the detriment of Sri Lanka, Minister of Strategic Development and International Trade Malik Samarawickrama said in a statement that the CEPA would not figure in the Lankan premier's agenda in New Delhi.