The boat is the suspected source of an infection in a New Zealand port worker.
Queensland Health Minister Steven Miles said all 19 crew aboard the Sofrana Surville have now been tested.
The ship was ordered to anchor off the coast of Mooloolaba instead of docking in Brisbane as planned.
The engineer's strain of Covid-19 had never before been detected in New Zealand, and has not been seen in Australia.
Miles said the New Zealand government has asked for Queensland to do genomic sequencing on the two crew members who have the virus to "confirm the information that they have to hand and to provide some further information".
"We will do that work ... which can take up to a week."
The two new cases will not be counted in Queensland's tally until they arrive on the mainland.
"There's a meeting under way to determine if they will be evacuated to the mainland, and what hospital that will be," Miles said.
The Sofrana Surville has a regular circuit between Brisbane, the Solomon Islands, Papua New Guinea, New Caledonia and New Zealand.
There are four active cases of the coronavirus in Queensland.