The government said three flights bringing Fijian nationals home would be allowed and passengers would be required to quarantine.
Prime Minister Frank Bainimarama said all local shipping services would cease from Sunday.
He said this was to help stop the coronavirus from reaching the outer islands.
Fiji Airways will operate its final scheduled flight between Nadi-Narita tomorrow, and the return Narita-Nadi on Saturday.
The airline said this flight was to assist citizens and residents to return home to Japan, as well as bring Fijians based in Japan back.
From Nadi only Japanese citizens and residents would be able to board the flight.
From Narita - only Fiji citizens, residents, staff of the UN and EU, work permit holders, and diplomats would be able to board.
Flight attendants invesitgated for breaching quarantine
Meanwhile Police Commissioner said 36 Fiji Airways flight attendants were being investigated for breaching quarantine rules.
During their 14-day quarantine in Nadi, the attendants were reported to have held grog sessions with other people, as well as receiving deliveries and guests.
Police commissioner Sitiveni Qiliho said investigations were underway and charges were likely.
The country's first case of Covid-19 was a Fiji Airways flight attendant, and all of Fiji's five cases arrived via the airline's flights.
More Covid-19 infringements
Three people are due to appear in a Suva court today charged with allegedly spreading false information on social media in relation to the Covid-19 situation.
The 32 year old, 36 year old, and 53 year old have all been charged with one count of Malicious Act Contrary the Public Order Act.
All are alleged to have posted false information on social media in relation to the coronavirus which created panic and fear among the general public.