Fijian authorities Wednesday denied claims they ordered the Sea Shepherd vessel Brigitte Bardot to leave its waters a week after the anti-whaling group's trimaran berthed for repairs.

Brigitte Bardot skipper Siddharth Chakravarty said he was told by Fijian officials the vessel had to go and was escorted out of Suva harbour by their naval vessel.

"The navy and immigration officials came on board and told us that we needed to depart the country," Chakravarty told local media after the vessel departed on Tuesday.

"At noon, they escorted us out from the Royal Suva Yacht Club."

However, Fiji Navy Commander John Fox disputed the claim by the conservation group.

"The Fiji Navy has had nothing to do with this group. I don't know anything about this" he told AFP.

Fiji's Immigration Director, Nemani Vuniwaqa, said the involvement of his officers was only to ensure proper procedures were followed before the Brigitte Bardot departed.

"The department conducted their job in clearing the vessel before it left our country. We just played our part. We don't know anything about the matter."

Earlier this year the Fiji government issued a statement saying it took protection of the environment seriously but "radical international groups" such as Sea Shepherd were not welcome in its waters.

When the Brigitte Bardot arrived in Suva last week the government would not comment but Chakravarty said they had berthed for repairs.