A trawler named Ann Mishal was intercepted with 77 on board in the western seas off the West coastal town of Chilaw while 21 more on board another unnamed trawler were intercepted eastern waters off the eastern coastal town of Batticaloa, the Navy said.
The arrested are to be handed over to the police for further investigations.
Sri Lanka in June launched special coordinated operations to nab illegal immigrants to Australia after recurring cases.
Faced with an influx of asylum seekers on board trawlers doing a risky sea voyage, Australia early this month said they would set up off shore centres to process asylum applications.