They also raise questions about military air traffic control procedures at the Resolute airport on August 20, 2011.
But any connection between the board's concerns and the fiery crash, which also sent three people to hospital, remains speculative, said director of air investigation Mark Clitsome.
"We're investigating as part of our report as to where the aircraft were and where they were going," he said Tuesday. "It's too early to say."
A clearer picture of the last moments of the fatal flight has emerged from the two aviation safety advisories from the board, which were written earlier this year. One advisory discusses military air control over the Resolute airspace.
Normally, Resolute is an uncontrolled airport, meaning pilots land using their own instrumentation and best judgment. But the military had planned to practise responding to an airplane accident as part of its annual Operation Nanook manoeuvres.
"In preparation for this, the military, for the first time, was going to take over the air traffic control duties at Resolute," said Clitsome.
That made Resolute a Class D airport, meaning pilots must ask permission and take instruction from air traffic control before landing. Pilots were notified of the change through Nav Canada.
However, the military radar system had not been completely installed and checked out and was not in use that day.
Civilian air traffic controllers have fallback procedures they use to instruct approaching aircraft and keep them a safe distance apart in the absence of radar. Because this was the first time the military had taken over a civilian airport, there was no such Plan B, said the board.
"The planning for this operation did not include the contingency for the provision of (instrument flight rules) services in a non-radar environment," the advisory says.
Military officials were not immediately available for comment.
Fog, cloud and drizzling rain meant both planes were depending on their instruments to approach Resolute. The board's interim report on the crash revealed the First Air 737's landing gear was down and locked and the flaps on its wings were open.
Three minutes before Flight 6560 hit the ground in its catastrophic crash, the second aircraft — another civilian plane — entered the airport's control zone "without appropriate IFR separation," says the advisory.
"There was a loss of separation and had the First Air flight not hit the ground there could have been a risk of a mid-air collision."
Clitsome said the military has since promised to alter its procedures.
Investigators have recovered First Air 6560's flight data recorder and it contains "good data," he added.
The issue of air traffic control is at the centre of several lawsuits that have been filed against the Canadian Forces over the crash.
The lawsuits claim there were several planes coming into the airport, but the military did not have enough people on duty to handle the traffic. The suits allege those working the tower were not briefed or properly trained to navigate civilian planes.
They also detail how soldiers communicated with the crew of First Air 6560 and gave the plane permission to land.
None of the allegations has been proven in court and statements of defence have not been filed.