Yes. In addition to embezzling from government agencies and government programs, it is also a federal crime to embezzle from certain private entities. For example, 18 U.S.C. Section 656 establishes the offense of 'Theft, embezzlement, or misapplication by a bank officer or employee,' and 18 U.S.C. Section 666 establishes the offense of 'Theft or bribery concerning programs receiving federal funds,' which includes programs administered by private institutions.
Under 18 U.S.C. Section 654, federal employees can also face embezzlement charges for stealing or converting money that comes into their possession as a result of their position in the government. This would include, for example, an agency employee embezzling fees paid by private citizens or businesses.