The closure was reported after a confidential Cabinet Paper was leaked to the Samoa Observer.
A statement from Fiji Airways confirms the issues of "partnership" and "codeshare agreements" are being negotiated between the two airlines.
"Discussions have taken place between Samoa Airways and Fiji Airways Executives on partnership and codeshare arrangements," the statement said.
The airline said it has now referred the matter to the Fijian government for its attention.
It is not clear when the inter-governmental talks on the Air Services Agreement will take place and the Samoa government has not indicated when it will close the lucrative route.
The Cabinet paper proposes travel to and from Fiji will be routed through Auckland using Samoa Airways.