A series of briefings given to the country's top air force commander last year expressed concern that the F-35's radio and satellite communications gear may not be as capable as that of the current CF-18s, which recently went through an extensive modernization.
Military aircraft operating in the high Arctic rely almost exclusively on satellite communications, where a pilot's signal is beamed into space and bounced back down to a ground station.
The F-35 Lightning will eventually have the ability to communicate with satellites, but the software will not be available in the initial production run, said a senior Lockheed Martin official, who spoke on background.
It is expected to be added to the aircraft when production reaches its fourth phase in 2019, but that is not guaranteed because research is still underway.
"That hasn't all been nailed down yet," said the official. "As you can imagine there are a lot of science projects going on, exploring what is the best . . . capability, what satellites will be available."
Additionally, Canada's request to have the upgrade placed in the fourth phase will compete with software changes sought by other countries. Norway, for example, wants to use its own missiles on the F-35 rather than U.S.-made weapons.
Defending the Arctic is one of the Harper government's key justifications for buying the aircraft, which are estimated to cost between $16 and $30 billion, including long-term maintenance.
A Defence Department spokesman denied that the F-35's communications suite will be less effective than that of CF-18s, but acknowledged that so-called beyond-line-of-sight communications is a concern.
"Communications in the Arctic represents a specific challenge to all aircraft due to lack of satellite coverage in the north," said Evan Koronewski in an email response. "Canada is working closely with the other partner nations to ensure Canadian operational requirements for communications in the Arctic are met."
Air force planners recognized the problem last year and are "considering a back-up," said an April 2010 briefing.
A study is looking at whether an external communications pod can be installed on the F-35.
Koronewski said it is one of "many options" being investigated, but wasn't able to discuss other potential solutions.
The sophisticated pods, which are carried by the CF-18s, were purchased as part of the $2.6-billion fleet upgrade, which began in 2000.
The briefing to the chief of air staff noted that installing such pods could be made more affordable if other countries participated.
The communications problem is just one of several technical issues the air force is working on.
National Defence has asked the U.S. manufacturer whether it's possible to install a different air-to-air refuelling system on Canadian F-35s. Most other air forces in the world have stopped using what's known as a "probe and drogue" connection, opting instead for a plug-in receptacle which connects to a boom on the tanker aircraft.
The request was made because it's unclear when Canada will able to upgrade its air-to-air refuellers with the booms. Lockheed Martin says it can equip the F-35s to use both systems, but a decision on whether to spend money on modification has yet to be made.