Mr Harris said the incident was technically a "near miss" but raised significant safety concerns.
"We are very concerned that an RPAS pilot appears to have allowed their aircraft to fly in such close proximity to a passenger aircraft," he said.
Today the NZALPA, which represents 2500 pilots and air traffic controllers, released a statement this morning saying it was relieved that no-one was injured and that no damage occurred.
It has previously registered its concerns regarding drones with the Civil Aviation Authority.
"Coupled with an almost complete lack of pro-active education by the Civil Aviation Authority, it is alarming that an uninformed person can purchase a drone and operate it near an aerodrome, seemingly with little idea of the seriousness of their actions should the drone hit or come in close proximity to another aircraft," said association air traffic control director Jon Brooks.
"The management of drone activity is adding additional workload and complexity for our air traffic controllers and pilots, and incidents such as this put those controllers and pilots in stressful and potentially harmful situations.
"Our members fear that we will continue to see an increasing number of these type of occurrences unless more restrictions are placed around the use of drones and that the Civil Aviation Authority starts to actively educate the New Zealand public on a large scale.
NZALPA was calling for the compulsory installation of "see-and-avoid technology" on drones, the compulsory addition of identity markings on drones as well as a comprehensive education program for all drone operators, not just co drone operators.
Harris said: "The RPAS should not have been anywhere near the Jet. It simply shouldn't have been in that airspace."
"We have to assume that this RPAS pilot was unaware of the rules regarding flying unmanned aircraft. While RPAS technology is advancing quickly and offers some very significant benefits to a range of industries it can pose a threat to conventional aviation activities and this must be carefully managed."
Transport minister Simon Bridges said the incident was being treated seriously.
"While this reporting is concerning, I am satisfied that it is being investigated fully, with urgency, and is being treated very seriously," Mr Bridges said.
A new civil aviation rule for RPAS, which came into effect on August 1, requires anyone who wants to fly a RPAS beyond what is allowed for traditional model aircraft - such as at night, beyond line of sight or above 400 feet - to apply for certification from the CAA.
"Unsafe RPAS flights are unlawful and will be dealt with accordingly," said Mr Bridges.
CAA investigators are working locate the RPAS operator.
In a statement Air New Zealand said it was disturbed by the "emerging trend of a reckless use of drones that puts the safety of customers and staff at risk".
Captain David Morgan said the airline will support any moves by authorities to ensure drone operations do not compromise the integrity of airline operations.
"Last night our customers and staff were put at risk as one of our aircraft departed Christchurch airport," he said.
"What our pilot believed to be a drone was being operated in and around the flight path but was fortunately spotted by our pilots who ensured the aircraft avoided it. This was reckless behaviour by the drone operator who has so far not had the courage to come forward and address their behaviour with authorities."
Captain Morgan said the safety of his airline's customers and crew was non-negotiable.
"Drones are an emerging issue for airline operators and clearly incidents involving drones are a cause for concern," he said.
"We welcome the prompt CAA response and investigation into the incident, support the authorities taking action against anyone who can be identified and encourage stricter industry regulation governing the operation of drones."
Under CAA rules, RPAS must not fly above 120 metres unless certain conditions are met, the craft must weigh less than 25 kilograms and it can only be flown during daylight hours.
RPAS operators must also be able to see their craft at all times and are restricted from flying in controlled airspace without the approval of air traffic control.
