The present invention provides for disambiguating the phase of a field received from a wireless tracker in an electromagnetic ("EM") tracking system. In a first method, a carrier wave signal is modulated with a tracking signal transmitted by an EM tracker. A time reference indicating a starting point for a particular phase of the carrier wave signal is determined and is used to determine the proper phase for the tracking signal. In a second method, the EM tracker transmits auxiliary data that includes the proper phase of the tracking signal. In a third method, the EM tracker includes a passive transponder that receives a desired phase of a tracking signal as auxiliary data in an excitation signal. In response, the EM tracker transmits the tracking signal according to the desired phase. Tracking electronics may then lock onto the proper or desired phase determined according to any of the disclosed methods.