The 28-year-old England international has been nursing a groin problem and sat out the trip to Norwich on December 28 as a result.
Rooney returned to the side for the New Year's Day home defeat to Tottenham, but was pictured on Friday leaving a private hospital in Manchester having had further scans to establish the extent of the injury.
United have given no update on Rooney's fitness, but Moyes has already decided that he will not face the Swans, although he could feature in the Capital One Cup semi-final first-leg clash with Sunderland at the Stadium of Light on Tuesday.
"He's got a groin injury and won't be available on Sunday. He's got a chance of facing Sunderland," said Moyes.
Rooney appears unlikely to enter into negotiations over a contract extension with United until after the World Cup which could be a concern for United if they fail to secure a Champions League place for next season.
"We would have to wait and see what [would] happen if that situation arose," said Moyes.
"But if you looked at his performances you'd have to say he's certainly playing at his best."