The travel arrangements were paused after a Kiwi woman infected with the highly contagious South African variant of Covid-19 travelled to about 30 locations in New Zealand before testing positive.
The initial 72-hour suspension was extended on Thursday, but flights will now recommence this afternoon.
There were no new community cases reported in New Zealand today.
The Australian Health Protection Principal Committee (AHPPC) noted today that there had been no further confirmed cases of Covid-19 in the community in New Zealand since the initial three cases were infected with the South African strain.
"As you know, the three cases all originated from transmission within hotel quarantine at the Pullman Hotel in Auckland. The AHPPC has also noted that all close contacts of these three New Zealand cases have returned negative test results and there have been no further cases found to date in the casual contacts, in the previous residents of the hotel or in the staff of the hotel," Kidd said.
"Green zone flights from New Zealand into Australia are now judged to be sufficiently low risk, given New Zealand's strong public health response to Covid-19.
"Given there is still a small risk of further associated cases being detected and with an abundance of caution, I've recommended to the Australian government that pre- and post-flight screening be implemented for all safe travel zone flights from New Zealand for the next 10 days."
As well as being screened for possible symptoms of Covid-19, Kidd's proposed pre- and post-flight screening will check that travellers have not been identified as close contacts of the infected cases and have not visited any of the contact tracing areas of interest in New Zealand.
"If they have, [the screening will check] they have been tested and they have received negative test results and clearance as required by the New Zealand authorities.
"Currently, to be eligible to fly on a safe green travel zone flight to Australia from New Zealand, passengers must have been in New Zealand for the previous 14 days.
"I've also recommended to the Australian government that time spent in hotel quarantine does not form part of the required 14 days in New Zealand.
"This means that people arriving in New Zealand and spending time in hotel quarantine must have been released from hotel quarantine for at least 14 days before they are eligible to take a green safe zone flight to Australia.
"The AHPPC will continue to monitor the situation in New Zealand very closely and we will receive daily reports from the New Zealand health authorities on the results of the continuing contact tracing related to this outbreak."