The selected design will then go up against the current flag in a second referendum, expected to be in March next year.
The flag panel's immediate task is to choose a preliminary long list of about 50 to 75 flag designs by the middle of next month.
Flag Consideration Panel chairman Professor John Burrows said thank you to the thousands of people who had submitted flag designs.
"As expected, there are hundreds of designs that have come in just ahead of the deadline and these will need to go through the same robust checking process as others to ensure they meet the guidelines and terms and conditions," Professor Burrows said.
The final count would be completed within 48 hours, and the final number could reach 10,000.
Mr Burrows said the longlist would be released in the interests of transparency.
"I think we owe it to the public what it has come down to in terms of the 75 - you can't just suddenly shut the door."
It would be impossible not to note public feedback, Professor Burrows said, but the release was not done to assess public support for each design.
"The Panel will then look at how the designs suggested bring together values and our identity as a nation," Professor Burrows said.
"There are also a large number of other factors we need to consider in this rigorous process from a practical and technical perspective, to ensure designs would be workable and 'fit for purpose', as well as meeting the principles of good flag design.
"The Panel will announce the preliminary long list of between 50-75 designs by mid-August and the four alternatives that the public will rank in the first referendum will be announced by mid-September," Professor Burrows said.
Unscientific polls have been carried out on nzherald.co.nz and other websites on flag designs, and opinions offered on social media activity.
Asked if that could influence the panel's choices, Professor Burrows said members would "certainly know it's there".
"We have regard to it. But we have to recognise that polls are a relatively small sample and can vary from time to time."
Other unofficial websites have been set up to further the debate, including flagtest.nz.
(App users click here to see the flags)
- Additional reporting from NZME News Service