The boat was seized in the sea 25 nautical miles west of Mathagal in the Jaffna peninsula, the Sri Lankan Naval spokesman said.
The Navy said that the gold was allegedly being smuggled into India. Two persons have been arrested in this connection.
On Monday, the Navy had also seized 1.7 kgs of gold hidden in a boat anchored in the Mathagal shore line.
These detections have raised suspicions of an organised gold smuggling racket to India from Sri Lanka, the Navy said.