...The NTSB warned of that danger in a safety alert for pilots last December.

“Using the autopilot can hide changes in the handling qualities of the airplane that may be a precursor to premature stall or loss of control,” the safety board said. “Turn off or limit the use of the autopilot in order to better ‘feel’ changes in the handling qualities of the airplane.”

Steven R. Chealander, the agency commissioner who is investigating the crash in Clarence, said this week that this doesn’t mean pilots should always fly manually when icing conditions occur, or that the crew of Flight 3407 was wrong to be flying on autopilot.

It just means that flying manually can help the pilot “stay ahead of changes as a result of icing,” said Chealander, who added: “The FAA sees things a little differently than we do.”

Indeed, in a 2006 alert, the FAA did not specify so clearly that the autopilot should be used sparingly in icy conditions.

“Pilots should follow approved guidance for use of the autopilot,” the FAA said. “If not closely monitored, the autopilot may mask dangerous airspeed losses. When ice is accumulating on the airplane, the autopilot should be disconnected at least once every five minutes.”

Laura Brown, an FAA spokeswoman, said the two agencies are really not that far apart on the autopilot issue.

“Our guidance is to periodically turn off the autopilot,” she said, stressing that the decision on how to fly may well vary from one aircraft to another.

“It may, in fact, be safer to fly with the autopilot,” she added.

That’s not the only issue on which the safety board and the FAA don’t see eye to eye....