Access-to-information documents suggest Chief of Defence Staff Gen. Walter Natynczyk has spent more than $1 million flying on the air force's Challenger jets since 2008, and one of those flights included a trip to St. Maarten.
But the military pushed back against the potentially damaging report Friday, noting that the Caribbean flight was authorized at a higher level and questioning figures used in a CTV News report.
Regardless, the prime minister said that the use of government aircraft for private business is allowed, as long as the treasury is compensated — something he has done in the past.
"Our government has dramatically cut the use of government aircraft," Harper said during an event in Saskatoon.
"When government aircraft are used, as certainly I do on some occasions, when they are used for personal or private travel, we expect that travel at commercial rates to be reimbursed to the taxpayers. That's what I do and that's protocol I think should be respected across government."
Harper said his staff would look into the general's use of the VIP jet.
Natynczyk did use the aircraft to join his family on a Caribbean vacation in January 2010 after missing his charter flight because he'd stayed behind to take part in the Trenton, Ont., repatriation ceremony of four Canadian soldiers and a journalist killed in Afghanistan, a senior defence spokesman said Friday.
More importantly, Lt.-Col. Norbert Cyr said the trip was signed off at a higher level, although he was unable to say who approved it.
"He was authorized to use the Challenger to link back up with his family," said Cyr, a spokesman for the Defence Department's Strategic Joint Staff. "Once you miss a charter flight, there are not a lot of options and this vacation involved a cruise."
Whether the general reimburses the treasury is "matter between the CDS and the prime minister," he said.
Natynczyk was travelling in Europe on Friday, and not immediately available for an interview.
Passenger logs, obtained by CTV News, show Natynczyk and some members of his family flew to Toronto from Ottawa for a Maple Leafs hockey game in appreciation of the military at a cost of $23,231.
Nearly $400,000 was spent going to six NHL games over three years and about $340,000 was spent going to CFL games.
Cyr says each of those trips fell within the realm of the general's duty and were wedged in between other official business.
CTV said Thursday that the Challenger costs $10,105 a flying hour to operate, meaning the trip to St. Maarten and back cost $92,956. The military countered by saying that figure is incorrect.
According to 2011-12 public accounts records, the total annual cost per hour of flying the VIP jet is $9,379. That figure includes the operating cost and the long-term, amortized expense of ground infrastructure. The per-hour operating cost is $2,321.
The report touched off a political storm with both opposition parties demanding more use of commercial flights by senior government officials.
"Peter MacKay is the (defence) minister. He has to answer for this," said NDP defence critic Jack Harris told CBC television.