The changes will take effect from April 4, 2018.
Rotorua Lakes Council expected the changes would attract more domestic visitors from Wellington.
It said Rotorua mayor Steve Chadwick had led efforts to reinstate the flights.
"Current flight schedules don't allow for that and we've lobbied hard on behalf of our business community," Chadwick said
"Air New Zealand has listened and it's now up to the local business community to support the new schedule and ensure it remains viable for the airline."
The announcement was welcomed by Rotorua Chamber of Commerce chairman John McRae who said reinstatement of the flights was a "coup" and a strategic priority for the chamber.
"The business community was seriously affected when they were removed and reinstatement has been a high priority," McRae said.
"A key role of the chamber is advocating for the local business sector. This is a great example of how we can work with stakeholders to help bring about positive change for the Rotorua business community."
He said that since the previous Wellington schedule was changed, business travellers have had to stay an extra night in Wellington, or travel from other airports, to get to early morning meetings in the capital.
Rotorua Airport chief executive Mark Gibb said the news comes on top of a strong performance from Rotorua Airport over the past year.
In the year to December 31, 2017, the airport recorded its highest number of passenger movements since 2008 – with 241,303 people travelling through the airport.
In December, the number of aviation movements also peaked at its highest monthly total since records began in 2012, with 537 aircraft using the airport over the month.
Peter Stubbs, who chairs both the Rotorua Airport board and the board of council's economic development organisation Rotorua Economic Development Ltd, agreed that the new schedule had come at the right time.
Air New Zealand's regional affairs manager, Ian Collier, said the changes came after consistent feedback from locals.
"We are pleased we have been able to achieve this for the Rotorua community after working closely with the local chamber, airport, council – and mayor Steve Chadwick. We are also delighted to add additional weekend capacity on the route which is a reflection of the strong growth we are seeing with Rotorua."