The air traffic controller at the helm when an Air Canada plane crashed into a rescue truck at LaGuardia Airport continued working after the deadly incident.

Only two controllers were on duty when two pilots were killed in the crash around 11:45 p.m. Sunday — but only one of them cleared the emergency vehicle to cross the runway to respond to an incident on another plane just as the Air Canada jet was landing, NTSB chairwoman Jennifer Homendy revealed.

“We know that that controller was still on duty for several minutes afterwards. Normally, they would be relieved,” she said.

“We have questions about that. Was anybody available to relieve that controller? We don’t know that yet.”

Homendy warned against “pointing fingers at controllers and saying distraction was involved,” as some reports claimed the FAA was investigating.

The potential distraction was a United Airlines flight on which a mysterious odor had sickened crew members.

An air traffic controller had cleared a Port Authority Police Aircraft Rescue Fire Truck responding to the issue to cross a runway just 12 seconds before the Air Canada jet touched down.

“Stop, stop, stop, stop,” a controller demanded, according to heart-stopping audio from the tower. “Truck 1, stop, stop, stop. Stop, Truck 1. Stop.”

A controller can be heard later in the audio admitting, “I messed up.”

“We rarely, if ever, investigate a major accident where it was one failure,” Homendy said. “When something goes wrong, that means many, many things went wrong.”

The NTSB is still investigating who was in the tower at the time of the crash, which killed two pilots and injured 40 people, including a flight attendant who survived being flung 300 feet.

Having two controllers on duty in the control tower is typical for a late-night shift, according to Homendy. Both were early into their shift when the crash happened.

The tower at LaGuardia had been busier than expected Sunday night because flight delays pushed the number of arrivals and departures after 10 p.m. to more than double what was scheduled.

The bodies of the two Canadian pilots — Mackenzie Gunther and Antoine Forest — will be held at a funeral home in Queens before they are transferred back to Canada.