The Defence Force said the formation leader had been charged "with negligently failing to perform a duty" although it did not allege the breach directly caused the accident.
It said Flight Lieutenant Pezaro "negligently failed to abort the mission" as weather conditions worsened.
The charge follows a separate safety-based review which found widespread safety and command problems, as well as a reckless culture at Ohakea's 3 Squadron.
Mr Carson said he was pleased there was some accountability, but believed those holding higher office should be held responsible.
"He is being made a sacrifice."
Former squadron leader Rob Stockley, who was the subject of an earlier failed court martial after signing out the fatal flight, said the charge was disgusting.
He said last night the practice of low flying in bad weather was well-known among commanders at the Ohakea-based squadron at the time, as was borne out by an inquiry at the squadron held a year before the fatal crash.
The inquiry in that case focused on one senior commander who "had a leading influence on the squadron at the time".
"The squadron was notorious for achieving above and beyond where anyone else would or could," Mr Stockley said. "The commanders knew and they failed to put adequate safety systems in place."
Mr Stockley, who tried to warn senior commanders of the dangers of low flying in bad weather, said there was "a long line of responsibility down the command chain".
"There is so much wrong with the whole concept of [Flight Lieutenant Pezaro] being charged at all."
Defence Force officials would not comment beyond the media statement about the charges.
The Herald revealed last year Flight Lieutenant Pezaro had written to the widow of one of his colleagues to explain how practices had changed at 3 Squadron and there were now hard rules about weather flying.
"This wasn't clear before Anzac Day," he said
He also said there had been training gaps on bad weather flying - a claim backed up by the military court of inquiry report.
Flight Lieutenant Pezaro wrote in the letter, sent two months after the crash, that the court of inquiry would find blame up the command chain.
"I'll be responsible in some part for leading the formation into the bad weather, the [commanding officer] and execs will be responsible for the crews' training and preparedness for the flight, even the [Chief of Air Force] will have his part to play in engendering the 'can do' attitude ... which caused us to push limits."
His court martial is to be held early next month.
