Malekula has been on lockdown since Sunday after the ship was found to have gone there to collect copra and had interacted with the community.
Authorities ordered the Filipino vessel to Port Vila where it was found to be coronavirus-free.
Under current Covid-19 measures, ships were allowed to come to Vanuatu, but human interaction was prohibited between crew members and locals.
The Director of Public Health, Len Tarivonda, said although the ship had been cleared, a Malekula man who boarded the boat had other issues to deal with.
