OTTAWA—The radar screen Toronto’s Pearson airport told the heart-stopping tale of a looming disaster.

A radar scope in the control tower showed two targets — one of them an Air Canada Embraer jet about to land — on a collision course.

The controller, perched high above the runways and taxiways, could see the landing lights of the approaching jet. But the identity of the other target was hidden in the late-evening darkness.

Unfolding in the darkness at Canada’s busiest airport was a runway incursion, one of the biggest threats to aviation safety today. A Star analysis of Transport Canada data counted 5,677 incursions by aircraft, vehicles and pedestrians since 1999, averaging almost 400 a year.

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The controller issued urgent orders to the Air Canada crew to abort their landing to avoid the mystery target — instructions that were ignored.

On the radar screen, the two targets merged — a nightmare scenario for any air traffic controller.

The Air Canada aircraft touched down safely, its crew oblivious to their near-brush — their flight had passed less than 50 feet over a van that had driven into their path.

The March 11 incident was “very close,” an investigator said later.

Just over a week later, pilots of a Boeing 727 cargo jet at Hamilton airport are told to abort their take-off roll. The jet slows to a stop halfway down the runway — ahead are two snowplows.

And in April, a controller at Pearson twice orders the crew of a commuter jet to stop on a taxiway. Yet they continue and intrude on an adjacent runway just as a Sunwing Boeing 737 jet is taking off.

While aviation has been getting safer, runway incursions — when aircraft or vehicles blunder on to an active runway or even taxiway by mistake — remain a weak spot.

The Transportation Safety Board of Canada has warned about “potentially catastrophic outcomes” of incursions.

“There is ongoing risk that aircraft may collide with vehicles or other aircraft on the ground at Canadian airports,” the safety board warned in one report into a close call at the Calgary airport in 2010.

The worst aviation accident ever was a runway incursion at the airport in the Canary Islands, when a departing Boeing 747 collided with another jumbo jet on the runway, killing 583 people.

“It’s a concern worldwide,” said Mark Clitsome, director of air investigations for the safety board, the independent agency that probes transportation occurrences.

“We’ve been watching those numbers for last few years and they’re not going down. So we’re concerned,” he told the Star in an interview.

The safety board has put runway incursions on its watchlist of transportation problems that pose the greatest risk to travellers.

There are many reasons for an incursion. In the case of the Air Canada near-miss, the van had been left in gear when parked at a nearby gate and had rolled across the runway without its driver.

More often, inattention and confusion are to blame. Pilots can lose their way in the maze of taxiways or in a moment’s inattention neglect to hear a controller’s instructions. Radio communications can get mixed up. Airport signs identifying runways and taxiways can be confusing. Vehicle drivers get lost.

“A lot of these airports have multiple taxiways and multiple turn-offs from runways. At night, in poor weather or if (pilots) get busy, they could wind up turning onto the wrong taxiway . . . or crossing a live runway,” Clitsome said.

But technology plays a part, too. The safety board has flagged problems with the radar system that monitors surface movements at Toronto airport and warns controllers of potential conflicts.

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The system was “at its limits” and outdated software means the radar “provided insufficient warning time to avert a potential collision,” the board warned after a 2007 investigation into an incursion.

Yet six years later, the recommended upgrades have yet to happen, the Star has learned.

Statistics prepared by a working group to curb incursions counted 1,078 incidents between Jan. 1, 2010 and Dec. 31, 2012. Of those, 126 were blamed on air traffic control, 651 were because of pilot errors and 301 were blamed on pedestrians or vehicles.

“This is an industry that involves a lot of humans and therefore we always have to be conscious of the human error element,” said Rob Thurgur, assistant vice-president, operational support for Nav Canada, the agency that operates the country’s air traffic control system.

“That’s . . . why we have the procedures and the vigilance that is trying to mitigate the human error out of the aviation system,” he said in an interview.

Thurgur also stressed that incursion statistics need to be viewed in context, noting that in most incidents there’s no risk of a collision.

Indeed, of the 1,078 incursions in the last two years, only four were classed as “extreme risk.” Another 16 were deemed “high risk,” 437 had “some risk” and the rest — 621 — had little or no risk, according to numbers compiled by the working group.

The safety board concedes that the chance of an incursion leading to a crash remains “relatively rare.” But it still warns that the “consequences can be catastrophic” because of the chance for a high-speed collision.

The Air Line Pilots Association International has warned that the “risk of a runway incursion event that could kill hundreds of people in a single accident is real and growing larger” because of increasing air traffic.

Nav Canada is heading a working group that includes airline pilots, airport operators, the safety board and Transport Canada to look at curbing incursions.

“We work collaboratively together to come up with the best phraseology, the best signage, the best documentation and the best technology and the best operation and procedures so we can minimize the risk,” Thurgur said.

He said technical troubles have delayed the upgrade of the ground radar system at Pearson urged by the safety board. Originally scheduled for last September, it could be early fall before the new system is ready.

“Because of the complexity of these systems, they don’t just go in overnight,” he said.

“We frankly ran into some software complications and we’ve had to make some changes. We’re still working towards making that upgrade,” Thurgur said.

By late summer, Nav Canada is also planning to add an extra layer of surveillance at Pearson, using aircraft radio transponders to track their position on the airport. The system is already up and running in Montreal and Calgary.

Data analysis by Andrew Bailey

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