INS Sutlej, a survey vessel, sailed for Colombo from Southern Naval Command in Kochi.
Another ship, INS Sunayna, a Naval offshore patrol vessel, will be leaving soon with more relief material, Navy officials said.
Over 40 people were killed and more than 400,000 people affected due to the heavy rains and landslides in various parts of the island nation in the last few days.
Heavy rains have been caused by cyclone Roanou in the island nation.
The cyclone has also put coastal states in India on high alert.
Prime Minister Narendra Modi had condoled the deaths on Thursday and had said that India stands “resolutely to help the government and people of Sri Lanka. Assistance being rushed on emergency basis”.