"We appreciate that New Zealand is continuing its investigation," he said.
"However, it remains a concern that the source of the infection in the community remains unknown; these cases have not travelled internationally nor have been in quarantine facilities."
Australia suspended its one-way quarantine-free travel bubble with New Zealand on Sunday following the discovery of new community cases in Auckland.
It did the same on January 25 when the South African Covid-19 variant was identified in the Northland community case.
It then extended the pause on January 28 before lifting it on January 31.
On this latest pause, Kelly said he and the Australian Health Protection Principal Committee (AHPPC) would provide revised guidance every 24 hours as further testing results become available in New Zealand.
"Three new cases tested positive on 16 February 2021[in New Zealand] bringing the total cases in the cluster to six," Kelly said.
"Time is required to complete the testing of contacts of the first three cases and contact tracing of the three new cases to determine if there is any spread in the community and the potential risk from people travelling quarantine-free to Australia.
"A further 72-hour pause provides the time required to confirm this cluster remains contained."
On Wednesday afternoon, Prime Minister Jacinda Ardern announced New Zealand would shift down an alert level.
Overnight Auckland moved to level 2 and the rest of the country to level 1.
Director general of health Ashley Bloomfield said it was reassuring that the latest Auckland community cases were linked and identified through contact tracing.
He said "we should be encouraged" that all cases have clear epidemiological links.
