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Auckland-based charter company FlyDirect will operate three aircraft on a schedule from the two cities, with a 35-seat Dash 8 aircraft from Christchurch and a 50-seater plane from Wellington.
FlyDirect.co.nz director Jef Kay said the company had been working for the past year to firm up package deals with Wanaka's accommodation providers, tourism operators and businesses.
A daily charter from Christchurch would offer morning and afternoon flights.
Daily morning trips from Wellington would be boosted around the weekends with afternoon flights also available from the capital on Fridays, Sundays and Mondays, he said.
About 25 full-time jobs would be created by the company, with offices and a terminal capable of catering for the expected 85-person capacity flights soon to be installed at Wanaka airport, Mr Kay said.
Lake Wanaka Tourism general manager James Helmore called the new charter flight service a massive boost for the local tourism industry.
"It's fantastic. There's no other way to describe it.
"Increasing flight capacity into Wanaka is our No 1 strategic goal," he said.
Charter flight packages included compulsory accommodation, with more than 30 options available at luxury lodges, hotels, motels, and backpackers, Mr Kay said.
"We're not a commercial airline service.
"People will have to buy a package when flying from Wellington and Christchurch," he said.
However, outbound passengers flying return from Wanaka would be catered for to allow local business people to conduct business in either city, Mr Kay said.
Wanaka Chamber of Commerce president Leigh Stock said the "back-fill" flights from Wanaka were an opportunity to see if an uptake from residents using the service would encourage commercial air operators to increase flight capacity.
flyDirect launched its website on Monday and early inquiries about the service had been promising, Mr Kay said.