Schools officials say Brad Niesluchowski, who was Higley Unified School District's information technology director, downloaded free software on district computers in 2000.
The program, known as SETI@home, uses Internet-connected computers worldwide to analyze radio telescope data in an experiment to find extraterrestrial intelligence.
But Superintendent Denise Birdwell told the East Valley Tribune that the program also bogged down the district's system and interfered with technology use in classrooms.
Birdwell said it will take more than $1 million to fix the problem, including removal of the SETI software. She says police are conducting a broader investigation.
Niesluchowski resigned from the district Oct. 22.
His lawyer did not return calls for comment.
Information from: East Valley Tribune, http://www.eastvalleytribune.com