Vice Adm. Allen G. Myer relieved Cmdr. Jeffrey P. Wissel from command Monday of the Fleet Air Reconnaissance Squadron 1 (VQ1).
A spokeswoman for Myer in San Diego, Cmdr. Pauline Storum, said no details of the allegations are being released during the investigation.
Wissel had been commander of VQ1 since April 2011. Executive Officer Cmdr. David R. Sauve has assumed command.
VQ1 flies the EP-3 four-engine propeller plane, a version of the P-3 Orion. Based at Whidbey Island Naval Air Station, the planes are deployed to air bases around the world. They do not operate off carriers.
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