This article has been amended from an earlier version to add comments from the Federal Aviation Administration regarding the allegations against John Duncan and a change in the allegations from the federal official close to the investigation.

A senior Federal Aviation Administration official has forbidden inspectors who are trying to determine why a Horizon Air commercial jet mistakenly landed on a Pullman, Washington, airport taxiway from reviewing “critical” evidence: recorded cockpit conversations between that flight’s pilots, a federal official familiar with the investigation said.

A federal official familiar with the investigation said the directive came straight from the office of John Duncan, FAA’s head of flight standards who is in charge of the agency’s flight inspectors across the country. The source, who requested anonymity because of the sensitive nature of the probe, said that despite the cockpit voice recorder being quarantined by Horizon Air, inspectors investigating the incident have been prevented from listening to the audio of the pilot discussions.

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“It’s a cover-up from the FAA at the highest level,” the source said. “We don’t want this to happen again because next time they could hit someone and people will die.”

The source said last week that the directive came from Duncan himself, but on Monday amended the accusation to say it came from Duncan’s office.

ABOVE: Surveillance video shows Horizon Air turboprop landing on the taxiway during a rainstorm at the Pullman-Moscow Regional Airport on Dec. 29, creating a mishap that’s being investigated by the National Transportation Safety Board. CLICK HERE if you are having trouble viewing the video on your mobile device.

Greg Martin, assistant administrator for communications at the FAA, said Monday that Duncan made no such order.

“The allegations against Mr. Duncan are unfounded and have no basis in fact. Further, Mr. Duncan provided no guidance direct or indirect on whether to listen to the cockpit voice recorders in this incident,” Martin said. “Rather, we respect the statute and longstanding aviation safety protocols that govern the use of cockpit voice recorders.”

Last week, the agency had said it could not comment based on the ongoing investigation.

Martin stressed that the National Transportation Safety Board chose not to investigate this incident or listen to the cockpit recordings.

Martin added that a statute and established protocols govern the use of cockpit recordings, and senior FAA investigators “can recall no instance where the FAA has listened to a CVR that did not involve a serious accident” or where the NTSB balked at investigating itself.

“The reason the use of CVRs is so restrictive is that listening to them beyond the most serious circumstances could have a chilling effect on crew communications and could diminish their value as an information safety tool,” Martin said.

Nonetheless, Martin confirmed that the FAA has opened a probe into the incident, one that does not include listening to the cockpit tape.

“Separate from the NTSB’s decision, our investigation is ongoing, and we are collecting substantive information through a variety of sources, including extensive pilot interviews and data retrieved from the aircraft’s operating systems and the airport,” Martin said.

The wayward flight is the latest high-profile airport mishap involving botched landings, including three at San Francisco International Airport — one of which could have resulted in one of the country’s biggest air disasters. Experts have said cockpit voice recorders are critical to determining what caused flight crew confusion. In the end, the Dec. 29 incident at Pullman-Moscow Regional Airport ended with the Horizon jet, along with its 38 passengers and four crew members, landing safely with no injuries.

U.S. Rep. Mark DeSaulnier, D-Concord, has been lobbying for improvements to how aviation and airline officials collect and save the cockpit recordings, which are often lost if not immediately pulled because the audio will overwrite itself. After the three alarming SFO incidents and others across the country, DeSaulnier wrote the FAA and pushed for a public hearing on the issue.

“Oh man,” DeSaulnier said by phone Friday. “What are they hiding? Why aren’t they being more forthcoming?”

The congressman said his office was in the process of crafting a letter to the FAA asking for details about the Pullman incident.

On Dec. 29, Horizon Air Flight 2184 landed on the small airport’s taxiway during a driving rain storm that had shorted out the runway lights. Alaska Airlines, which operates Horizon, said the 17-year veteran pilot misidentified Taxiway Alpha as Runway 6 and landed. The airline also said the pilots have been temporarily suspended from flying during the investigation.

Because the Horizon plane actually landed on the taxiway, federal regulations require the airline to immediately report the incident to the National Transportation Safety Board and to preserve the critical data, including the cockpit voice recorder. The airline followed the rules, but the NTSB declined to investigate the incident.

It’s not always required that cockpit voice recordings be retrieved, and if they are not, they will be overwritten. That is what happened in the SFO near misses. In one case, an Air Canada plane narrowly averted landing on a taxiway crowded with four fully loaded jets awaiting takeoff. But because it didn’t land on the taxiway, the airline was not required to retain the recording and the plane took off hours later.

The FAA has initiated a probe in the Horizon Air incident, but that effort has now been diminished, according to the source.

“If I were doing it and I didn’t have all the information, I couldn’t close the investigation. It is that crucial. … The CVR will tell you everything,” the source said of the cockpit recordings. “(The FAA) flat out told them you can’t listen to that tape. To me, that’s very troubling.”

Interviewing pilots is helpful, experts have said, but the raw conversations leading up to the aviation error are pivotal.

“It helps us figure things out in case someone lies to us,” the source said.

Federal regulations require the recorder to be held for at least 60 days by the airline, unless the FAA releases it earlier. But the federal official said the concern is that once that period ends, the data could be lost forever.

“Then we’ll never know what happened.”