Virgin Australia is scrambling to accommodate thousands of passengers after the Samoan government blocked it from operating flights between the Pacific island and New Zealand.

Samoa pulled the plug on Virgin Samoa, a joint venture with Australia's number two airline, in May and is preparing to launch its own national carrier called Samoa Airways.

Virgin Australia said it was working with the Australian government to have the decision overturned. Credit:Glenn Hunt

Virgin Australia had planned to fly its own services from Australia and New Zealand to the Samoan capital Apia from November 13, but on Monday said that permission for Auckland to Apia flights had not been granted.

"Virgin Australia is disappointed with the Samoan government's decision to deny authorisation of our services," a Virgin Australia spokeswoman said.