SAN FRANCISCO — Just three months after an Air Canada plane nearly landed on a taxiway crowded with jets full of passengers, the Federal Aviation Administration has launched another investigation into why a plane from the same airline Sunday ignored a San Francisco air traffic controller’s repeated order to abort a landing.

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Watch: Exclusive animation reenacts Air Canada plane’s near-disaster at SFO Air Canada Flight 781, an Airbus A320, was preparing to land at San Francisco International Airport on Runway 28-Right on Sunday night after a six-hour flight from Montreal. The crew acknowledged the tower’s clearance to land when it was six miles from the airport, said FAA spokesman Ian Gregor.

However, as the plane approached, an air traffic controller repeated six times that the Air Canada pilot should execute a “go-around” — an aborted landing where the plane pulls up and circles around to approach again. There was no response, according to an air traffic control radio recording reviewed by Bay Area News Group. The tower ordered the go-around because it was not certain if an earlier arriving plane had fully cleared the runway, Gregor said.

“The Air Canada crew did not acknowledge any of the controller’s instructions,” Gregor said.

As the plane got closer to landing, a tower supervisor used a red light gun to alert the crew to abort the landing. A flashing light gun is “standard protocol” when an air crew is not responding to radio instructions, Gregor said.

However, despite all those efforts from the tower, the Air Canada plane still landed on Runway 28R at 9:26 p.m., Gregor said. Fortunately, radar showed after the fact that the Southwest Airlines jet the tower had feared was still on the runway had actually cleared the area.

After it landed safely, the Air Canada crew alerted the tower it had a radio problem, Gregor said.

“That’s pretty evident,” the air traffic controller told the flight crew. The controller then guided the plane to the proper taxiway, according to the radio recording.

The FAA is investigating the incident. The National Transportation Safety Board and Transportation Safety Board of Canada are aware of the incident but not investigating, spokesmen for those agencies said.

The official Air Canada twitter account initially sent a tweet to this reporter after a story about the incident first appeared online, appearing confused about what had happened.

By Tuesday, Air Canada released a statement, declining to comment on whether the flight crew was disciplined, or whether it involved the same pilot or co-pilot involved as the incident three months ago. The airline also declined to say whether that flight crew had been disciplined.

“After receiving proper clearance to land, it proceeded to do so and landed normally,” said Air Canada spokesman Peter Fitzpatrick about Sunday’s incident. “Upon landing, the crew was informed the tower had attempted unsuccessfully to contact the aircraft; however the message was not received by the crew. Air Canada is investigating the circumstances.”

Christopher Praught, spokesman for Air Canada’s pilots union, said the flight crew experienced a “communications failure after being cleared for landing.”

“Specifics regarding the nature of the communications failure are under investigation by the FAA,” Praught said in an email. “The aircraft landed safely, and preliminary information indicates the incident posed no risk to the aircraft, passengers or crew. The flight crew is working with the FAA to determine what transpired.”

Retired commercial airline pilot Ross Aimer said the incident left him shaking his head.

“Pilots must exercise extreme caution to make sure the runway is cleared of the previously landing traffic,” he said in an email. “In this case, because Southwest did not exit the runway in time, Air Canada should have promptly gone around, even without the controller telling them what to do. Radio discipline is extremely important as well. If one radio goes silent for any reason, there are other radios they can quickly switch to.”

In airport as busy as SFO, Aimer said he’d check his radio if he did not hear anything from the tower for more than 30 seconds.

“The tower even used the old-fashioned ‘red light signal’ as a backup, but these guys were clueless!” he said.

Shem Malmquist, a 777 pilot, said it was not surprising that the flight crew failed to see the light gun, which is transmitted from the airport control tower, because the SFO tower is so far from the runway.

“In over 40 years of flying the only time I have ever seen one was when I asked a controller to demonstrate the system for a student pilot,” Malmquist said in an email. “It would only be noticeable if the pilot was looking towards the tower, and absent knowing they would need to, doing so would add potentially dangerous distraction to an already-critical phase of flight.”

Sunday’s incident follows a stunning July 7 near-collision involving the same airline, airport and runway.

In that episode, Air Canada Flight 759 mistook a crowded taxiway for Runway 28R and flew as low as 59 feet off the ground before the pilot aborted his landing, flying dangerously close to four other aircraft awaiting takeoff with an estimated 1,000 passengers on board all the planes, according to an ongoing National Transportation Safety Board investigation. The flight crew later told investigators it thought the taxiway was actually their intended runway.

Aviation experts have said that near-miss could have triggered one of the worst aviation disasters in history. Officials did not initially report the incident, which allowed the cockpit voice recorder to be overwritten.

Federal investigators also determined that the Air Canada plane dropped off the air traffic controller’s ground surveillance system radar during its final 12 seconds on approach.

Since the close call, the FAA no longer allows visual approaches for aircraft approaching SFO at night with an adjacent parallel runway closed, according to the FAA. Instead, they must use instrumentation to land. In the tower, the FAA now also requires two controllers to remain in position during busy late-night hours, the agency has said.