The university has said it would file a request for the full board in Washington to review the decision. It has until April 9 to do so.
The federal labor agency does not have jurisdiction over public universities, so the push to unionize athletes has been primarily targeted toward private schools such as Northwestern.
Opponents say giving college athletes employee status and allowing them to unionize could hurt college sports and higher education in numerous ways.
Associated Press writers Tom Raum and Donna Cassata contributed to this report.
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