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This is related to a small single-engined plane.

On a recent flight, the controller kept telling me that I was 300 ft higher than it appeared on my altimeter and GPS (which were in sync). This was not a problem on the previous two legs of the flight. However, multiple controllers thought that my altitude was 300 ft higher.

Has someone run into this issue? What could be the problem?

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It sounds like there was an issue with your altitude encoder

The transponder depends on an external altitude encoder to provide the digitized pressure altitude that the transponder needs for its Mode C replies. The encoder is connected the same static air line as the altimeter and is wired electrically to the transponder.

AR-850 The encoder may be either a separate unit ("blind encoder") or integrated into the aircraft altimeter ("encoding altimeter"). Encoding altimeters save space and help ensure that the encoder and altimeter agree, but they are fairly expensive.

If you have a blind encoder its possible it can report erroneous information with out affecting other instruments onboard. You should alert your mechanic (or the mechanic that takes are of the aircraft in question) to have this checked.

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    $\begingroup$ The encoder/transponder has to be checked with test equipment, and a leak test of the static system done, every two years by an avionics AMO if you want to fly in transponder airspace in Canada. An encoder could easily drift in that time. $\endgroup$ – John K Jun 12 '18 at 3:41

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