The service has previously been privately run, it wasn't part of the region's public transport network, Metlink, or subsidised by ratepayers or taxpayers.
Under NZ Bus the service didn't accept Snapper, wasn't tracked by real-time information on the Metlink network, and was the subject of fares hikes.
In an upcoming Transport Committee meeting agenda GWRC officers said Metlink was best placed to operate the connection between the city and the airport because it could be integrated in with the region's wider public transport system.
They considered the airport to be an integral part of Metlink's network.
"Wellington Airport is a key regional destination providing an important connection linking the region with the rest of the country and to overseas destinations.
"The airport is also a major employer in the region. Even in the current Covid-19 context, the airport continues to generate journeys from across the region to access flights."
Wellington Airport's chief executive Steve Sanderson said they have been working closely with Tranzit to launch a new and improved service early this year.
"Having invested a lot of time in establishing this service, we are obviously disappointed Greater Wellington is proposing to take it over under the Metlink brand, but we are working with Greater Wellington to enable its service to begin as soon as practically possible.
"Unfortunately, the decision by Greater Wellington means a further delay to the start of a new service under the Public Transport Operating Model (PTOM) and new tender process is required."
Sanderson said the airport would work to deliver an improved service for travellers.
When asked why its partnership with Tranzit didn't go ahead and why GWRC took over, the airport referred questions to the council.
A GWRC spokesman said Metlink was able to put forward a PTOM service as part of the regional public transport plan because the commercial contract with NZ Bus had ceased.
GWRC chairman Daran Ponter said a new service wouldn't be up and running until mid-2022.
"Patronage to and from the airport is just so low at the moment that neither a fully commercial nor a subsidised service can really be justified."
The council also needs to follow its own processes, including requiring the future operator to use electric buses.
It will now include the new transport unit in its draft public transport plan, which will then be consulted on.
Once the proposal is locked into the final plan, the tender process can start followed by a lead-in time for the successful company.
Ponter said the price point for the new bus is likely to be more than Metlink's normal services, but less than what has been charged for the service in the past - about $12.
The service would run between the airport and the railway station, but not to Lower Hutt, Ponter said.
"What we are saying to the Hutt community, the Porirua community, and the rest of the Wellington City community, is that we will look to make sure our connections for services from those other points to the new Airport Flyer service are tightened up and more regularly available.
"So we are not forgetting those communities, we are looking to wire them in."
Ponter said the situation would be up for review if there was an influx of Flyer users connecting from other cities.
MP for Rongotai Paul Eagle says a return on the cards is great news for Wellington communities.
Eagle said the move was great news for Wellington communities.
"I look forward to a service that is well integrated and has all the latest payment and tracking features which were sorely missing from the service before it was halted. More importantly any new service needs to be well priced so it doesn't hit people in the pocket."
Hutt South MP Ginny Andersen said the move to align the bus with Metlink should have happened a long time ago.
"But I am incredibly disappointed that Lower Hutt won't be included and I'm not accepting that.