Let’s take a deeper dive into the NYPD’s recently aborted counterterrorism training trip to Afghanistan that resulted in two commanders being tossed off a chartered military flight, allegedly because they were drunk. Counterterrorism Chief James Waters then called off the operation.

The NYPD acknowledges that the six-man team, including Waters, a deputy chief and a captain, went for “a few” beers at the Baltimore-Washington International Airport on Aug. 10 after they learned their flight to Afghanistan had been delayed three hours. The NYPD’s Aviation Unit had flown the men down there.

When they boarded the military plane, the crew, which department officials say followed military protocol, apparently concluded that Deputy Chief Scott Shanley and Capt. Daniel Magee were too drunk to make the 14-hour trip. Waters notified the Critical Response Team in New York, which sent two vans to pick them up.

The department maintains the six were unarmed while drinking. If they were drinking while armed, that would be a major problem.

Contrary to some media reports that Magee was disruptive and yelling at the crew, the NYPD maintains he and Shanley did nothing to warrant being removed from the plane. A top department official who asked for anonymity because the incident is under investigation said, “Nobody ever made allegations to the NYPD or to Waters that anybody engaged in misconduct . . .”

Nonetheless, their actions are an embarrassment to counterterrorism Deputy Commissioner John Miller, the Counterterrorism Bureau and the NYPD. The incident also raises questions about Waters, who formerly headed the Internal Affairs Bureau’s notorious Group One, which handles misconduct and corruption investigations involving ranking officers. He’s made a lot of enemies. Although his reputation is that of a straight arrow and the department maintains he himself wasn’t drinking at the airport, one former top NYPD official familiar with such incidents questioned his “failure to supervise.”

“If he was there, he should have stepped in and stopped the drinking, no two ways about it,” said the former official, who asked for anonymity because he is not authorized to speak about the incident. “Remember, they were representing the NYPD and the city and have to be a cut above. Waters should get a reprimand of some sort.”

An investigation into the incident is being conducted not by the IAB but by Miller because no misconduct has been formally alleged.

That decision was apparently made by Commissioner James O’Neill.