A viral nightmare might soon be coming to an end for five Australian residents as the government confirms plans are in place to evacuate passengers from a stricken cruise ship.

A government-supported charter flight will carry four Australian citizens, one permanent resident and a New Zealand citizen to Australia from Tenerife in the Canary Islands after their voyage was marred by a deadly outbreak.

The MV Hondius docked in Tenerife on Sunday after three people died and five others were confirmed to have tested positive to hantavirus, which is contracted through contact with infected rodents.

Consular officers on the ground in Tenerife and in Canberra had been closely coordinating their response efforts, a federal government spokesperson said.

The Australians onboard are expected to be some of the last passengers to disembark, with the repatriation flight likely to leave the island about 5pm local time on Monday and arrive in Perth on Tuesday.