With new charges that one of its contractors mishandled government secrets, Booz Allen Hamilton Holding Corp. is facing its second major personnel scandal in three years.

The Justice Department on Wednesday charged Harold Thomas Martin, a Maryland resident, with stealing top-secret documents and unlawfully taking government property. Mr. Martin, a contractor for the National Security Agency, was employed by Booz Allen, according to people familiar with the situation, the same firm that employed Edward Snowden.

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