The restrictions came ahead of cyclone Yasa which hit the country last Thursday.
The category five storm left four people dead with the northern island of Vanua Levu bearing the full brunt of Yasa.
However, restrictive travel would remain for the Lau, Kadavu and Lomaiviti groups.
The maritime authority said any travels to these Islands must be approved by the National Disaster Management Office (NDMO).
In a public advisory, MSAF chief executive Simon Gravenall said all other maritime transport involving passengers and cargoes could resume.
