Money, in New Zealand dollars, was in the merchant's bank account in two days. However, Mr Freer said, the company expected the transfer time to drop to 24 hours in the next few months.
The only cost for a business was a 1.6 per cent merchant fee on every transaction.
The app also enabled businesses to push promotional offers, while users could research destinations to find where Alipay was accepted, claim vouchers ahead of travel and leave customer reviews.
After an information session in Queenstown yesterday, organised in conjunction with the Queenstown Chamber of Commerce and Destination Queenstown, Freer said the system would help increase Chinese expenditure in the South Island.
"By us not offering that type of payment facility for them here, we're leaving spend on the table."
Mobile payments had risen over the past five to 10 years as "the way of paying" in China. "It's only natural then that because there is such a low credit card adoption in China, when Chinese travellers look to travel internationally they want to pay using a way that they're used to at home."
Detailed information about the South Island Alipay transactions would be accessible by merchants, regional tourism organisations and other tourism bodies, to help them understand the Chinese market and create efficiencies in destination marketing.
"The great thing about this is we build up a profile of who our Chinese guests are in the South Island - where they're going, what they're experiencing and even demographically who they are - that we then use to both help refine the marketing that we do ... to target the Chinese customers that come to New Zealand."
To date the airport had run 20 information sessions across the South Island and Freer anticipated up to 1000 businesses would sign up to Alipay within a couple of months of the project going live.
"We know that for this to be successful that our Chinese guests need to understand that Alipay is widely accepted in the South Island, and to do that we obviously have to get a critical mass of merchants on board, and to do that we need to lower the barriers of entry.
"And that's why we've made it such a simple process for merchants.
"It's a significant investment on behalf of the airport, because we know that if we grow the wider economy of the South Island then we benefit as the airport from that."
Christchurch Airport is leading the country in growth of Chinese visitor arrivals - up 13 per cent for the year.
Total arrivals into New Zealand remained flat for the same period.
That was, in part, due to the partnership between the airport and China Southern Airlines, which began in December 2015.
The airline announced last month its direct flight from Guangzhou to Christchurch would go daily from December 2 to February 28, having previously announced five flights a week from October 10.
That meant almost 12,000 additional international seats to and from Christchurch over the peak summer season.
