The move expands the government's probe beyond Microsoft's practices in the web-browser market where the company has been accused of monopolistic practices by several industry partners.
Sun's Java software is seen as a potential competitor to the Windows operating system, and Sun's chief executive Scott McNealy is an ardent Microsoft critic. According to the reports, Sun has filed a civil suit against Microsoft alleging violations of its license to use Java.
A Sun spokeswoman would not reveal what information is sought in the subpoenas.
A Microsoft spokesman told ZDNet News it was not surprised by the subpoenas and said the company is confident it is living up to its contract with Sun.