The court had earlier ordered extension of remand of all the 34 fishermen, but in the evening it ordered the release of 29 of them and extended the remand of others, fisheries department officials said.
Regarding 31 others who were arrested, the court asked authorities to produce them on September 13.
The 65 fishermen were arrested on July 30 by the Lankan navy for allegedly crossing the International Maritime Boundary Line.
In another development, The Pamban Fishermen's Association today decided to intensify their 19-day old strike and called for closing of shops to press their demand for the release of 25 fishermen who were arrested on August 25 in South Sea area.