The Filipino victim was found dead "with severe cut injuries."
The initial investigation showed the victim was murdered after a dispute with the other sailors aboard the Taiwanese ship.
Six Filipino shipmates linked to the crime initially fled but later decided to surrender to authorities through the Philippine Embassy.
Colombo Harbour Police has started taking statements from the suspects with the help of a translator provided by the embassy.
Meanwhile, a Sri Lankan portal did not immediately name the victim nor the six who were arrested.Update:
The Filipino sailor has been identified by Sri Lanka authority