Pacific Blue is the subject of at least two investigations by aviation authorities after two incidents, two days apart, above Queenstown.

The Transport Accident Investigation Commission is investigating a June 20 incident in which Pacific Blue and Qantas aircraft travelled too close together in what is known as a "loss of separation".

Pacific Blue declined to comment on the matter last night, but TAIC chief investigator Tim Burfoot confirmed the two aircraft had come within 304 vertical metres of one another.

He said the Pacific Blue pilot was about to land in Queenstown but decided not to because of bad weather conditions, so moved out to do a "go around" before attempting to land again.

The loss of separation occurred as the aircraft was climbing. It is not known who is to blame and an investigation could take up to six months.

Meanwhile, the Civil Aviation Authority is investigating claims by four witnesses that a Pacific Blue pilot breached rules by departing Queenstown airport in dark, stormy weather on June 22.

A spokesman confirmed the airline was investigating the incident on the flight, but said the flight took off "20 minutes before evening twilight".

Sixty-five passengers and six crew were on board the aircraft.

But CAA spokesman Bill Sommer said investigators believed the flight was "probably 12 minutes late getting airborne".

Airlines operating out of Queenstown must depart no later than 30 minutes before twilight as a safety precaution because the airport was not lit at night.

The rule is in place because the mountainous surroundings and obstacles are hard to see and, if a pilot changes their mind about departing, they need sufficient time to land.

Mr Sommer said the investigation would look at all aspects of the flight, including the crosswind limitations of the aircraft, which he said was 16 knots (29.6km/h).

"It's been reported that the crosswinds when they got airborne may have been 20 knots."

Investigators would speak to the pilot, the airline and witnesses.

One witness, Queenstown harbour- master Marty Black, said it was "virtually dark" when the plane took off into a front. "Not only was it dark, but the weather was bad ... that's not a good mix at all ... it took off, it was airborne and it basically dropped in height. It didn't climb at all."

A Pacific Blue spokesman said: "The airline has an internal procedure that aircraft at Queenstown should take off a minimum of 30 minutes before evening twilight. On this occasion the aircraft took off about 20 minutes before evening twilight.

"After takeoff the aircraft climbed at a safe and legal height in accordance with the weather conditions at the time and followed the prescribed visual departure procedure to continue its course to Sydney."

Transport Minister Steven Joyce said he had been briefed on the incident and expected an investigation to take up to two months.

"Obviously it's a concern. Civil Aviation were very concerned at the time and they are undertaking this investigation. They've been talking to Pacific Blue about their operations."

- Additional reporting Derek Cheng and NZPA