Vanuatu's Prime Minister Bob Loughman announced the confirmation of the positive case by health authorities at Port Vila Central Hospital.
He said the government was issuing the order to ban outbound travel from Efate for three days while contact tracing efforts were conducted.
Loughman has appealed to the public to voluntarily test for the virus at Vila Central.
According to the director general of health, Russell Tamata, the hospital has sufficient tests kits for voluntarily testing.
As contact tracing began today, Tamata confirmed that 16 people have been put in quarantine at Ramada Hotel. Most of them are police officers who attended the scene when the body was discovered at Pango beach on Sunday, April 11.
Tamata said the risk of community transmission was minor.
Loughman meanwhile said business would operate as usual but appealed to the people to abide by Covid-19 safety protocols such as social distancing.
The dead body of the Filipino is still at the mortuary at Vila Central.
Vanuatu has reported only three previous cases of Covid-19, all at the border.