Southern DHB medical officer of health Dr Susan Jack, who asked WellSouth to undertake the tests, said it would "uncover any pockets of disease" so far undetected.
It followed 343 random tests taken last week of shoppers at the Queenstown Pak’nSave.
The aim, Dr Jack said, was to target high risk communities and those possibly not well represented in testing so far, including healthcare workers, Maori and Pacific people, and those with recent international travel.
She said testing would inform "the extent to which we can relax the restrictions we’ve been living with".
Almost all guests at Base Backpackers on Shotover St volunteered to take the test.
General manager Marvin Freeman said there were only 50 guests at the hostel, compared to a capacity of about 300.
"We sent a flyer to each dorm and posted in a group chat we’ve set up to keep guests notified.
"A couple of people didn’t want to take part, but most were really enthusiastic, it was awesome."
He said people in the hostel were getting along well, keeping to themselves, the common areas being closed and a roster for the guest kitchen.
"We have an on-site kitchen and a chef living in-house, so we have been able to do food deliveries to rooms."
The hostel has used three large screens in the reception to display the latest Covid-19 information and flyers were sent around regularly with updates.
Dean Ferguson (28), from Scotland, said testing backpackers was "a great idea".
"I got a bit worried when they said something was going up my nose.
"One nostril was very unpleasant, but the rest was all right."
Canadian Tonya Chang (28) also volunteered to be tested.
"It was not that bad. The nurses were so nice, funny and efficient."
A second hostel is to be swabbed today and a further two in the coming days.
The SDHB urged those with symptoms to call Healthline or their GP.
The random testing was for those without symptoms.
