The Minister of Works, Transport and Infrastructure, Papali'i Niko Lee Hang, said the Ministry of Police would take over the site.
The minister told the Samoa Observer all flights would now operate out of Faleolo International Airport.
Fagali'i Airport had failed to meet international standards and must be closed down for safety reasons, he said.
He said that Fagalii had also become the gateway for drugs smuggled into the country, with drug dogs only occasionally able to patrol.
Fagali'i' was unsafe and the runway was deteriorating.