Super Shuttles, a national franchise, charges $33 to take a single passenger from the airport to the Dunedin city centre, $8-$13 more expensive than its rivals travelling the same route.
One Otago Daily Times reader, who did not want to be named, said it was cheaper to travel on a bus from Dunedin to Christchurch than take a shuttle from Dunedin International Airport to Dunedin.
Bus fares between Christchurch and Dunedin - a distance of 360km - can be found at $19.
Late last year, Super Shuttle successfully tendered for airport licences, with the number of shuttle companies able to use the designated airport rank from October 1 reduced from 12 to two.
Other shuttle operators were still able to operate from a common rank but only after a scheduled aircraft arrival.
Previously, 30 shuttles were licensed to use the designated rank, but that has been cut to 14, with Super Shuttles operating 12 shuttles and Southern Taxis two.
Super Shuttles spokesman Graeme Dobson, of Auckland, said claims its fares were expensive came from other "disgruntled operators".
The company had not increased prices and was not running a monopoly. "Our pricing hasn't increased."
No complaints had been received by the company since the new airport licensing scheme began, he said.
The previous system needed an overhaul as several "individuals" had let the airport and customers down by poorly presented vehicles, aggressive drivers and inconsistent pricing structures, he said.
With thousands of university students expected to arrive in the city over the next few weeks, customers could save money on shuttles by using a ride-sharing scheme, where additional passengers going to the same address would be charged $8.
"Our marketing has been consistent around the student area. And we encourage students to share a ride," Mr Dobson said.
He said the firm's Dunedin's airport-to-city fare was more expensive than those it charged on other major cities' routes (Auckland's is $30, Hamilton's $24 and Wellington and Christchurch's are $17) because Dunedin's central business district was the further from its airport.
Calls to Dunedin International Airport manager John McCall were not returned yesterday, but the airport's website recommended passengers discuss costs before beginning a journey.
Mr McCall said in September changing the licensing system had been the right decision.
