The shutdown hit mostly the urban areas of the heavily populated Jaffna town with public transportation coming to a halt. Schools, offices and businesses remained shut.
The shutdown was organised as the Tamil groups accused the Sri Lankan government of going back on its pledge to release all the political prisoners by November 7.
They have demanded the release of the political prisoners and the repealing of the Prevention of Terrorism Act (PTA), which was implemented during the war in Sri Lanka.
The government said it was not possible to grant them a common amnesty while the possibility of granting them bail would be considered.
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Some 30 of them, held mostly for alleged links to the LTTE were, however, granted conditional bail yesterday.
The chief minister in the North CV Wigneswaran yesterday met President Maithripala Sirisena over the issue.
Sirisena has said that while it was not possible for him to intervene, due legal process would be followed to release the prisoners.
The Sirisena government faces political roadblocks in the Sinhala-majority South for agreeing to release those held for alleged terrorit activies.