Austin, Southampton's top scorer this season with nine goals in all competitions, missed Sunday's 1-0 Premier League win over Middlesbrough after being injured in Thursday's 1-1 Europa League draw with Hapoel Beer-Sheva.
"He needs surgery and will be perhaps between three months and four months [out]," Puel told reporters.
Austin, 27, has been a key figure at the club since joining from Queens Park Rangers in January for a transfer fee of four million pounds ($5.02 million).
Southampton's home victory over fifth from bottom Middlesbrough lifted Puel's side to 10th in the table.
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(Reporting by Neil Robinson; Editing by Tony Jimenez)
