The information comes after Queenstown Airport ran out of jet fuel last week, affecting two flights.
Earlier this month several airports ran out of avgas, which is used in sightseeing and private aircraft.
A customer says one shortage was longer than fuel companies have stated.
In a statement BP managing director Debi Boffa said the fuel was unavailable at Queenstown Airport for a few hours on March 2.
It was also unavailable at the Te Anau Airport Manapouri for a "period of time" on March 3.
"We would like to apologise for any inconvenience the situation caused.
"Safety is our first priority, and the delay in avgas supply was caused by a requirement to perform additional testing on the fuel, to verify it met all quality requirements.
"The tests were passed and allowed the fuel to be released to the airports following the normal process."
A Z Energy spokeswoman said "a number of sites" were out of avgas for "varying lengths of time" recently.
The company stocks Dunedin Airport, Wanaka Airport, and the Alexandra airfield.
The shortages were due to supply constraints in the South Island, she said.
Glenorchy Air quality assurance manager Pauline Leech said the company tried to refuel at Queenstown Airport on Friday, March 1, but was unable to.
The fuel was not restocked until Sunday afternoon, she said.
"What BP is saying is wrong, but to be fair, perhaps they weren't aware at first."
However, a BP worker on the ground knew of the shortage, she said.
The Civil Aviation Authority said it was notified about the shortages, but was not investigating.
"The CAA's concern is fuel quality, as this has the potential to directly affect flight safety, rather than fuel availability. In this case there was no apparent issue with fuel quality."
All airports contacted yesterday were unable to provide comment.
