Following consultation with a specialist, O’Donoghue underwent surgery last week for the knee ligament injury he sustained against Leinster in the Guinness PRO14 semi-final earlier this month.
The back-row forward is expected to follow a long-term rehabilitation programme.
Munster will have additional cover in the back row next season following the signing of Arno Botha from London Irish.
On the contract front, prop Jeremy Loughman will remain with the province for next season after signing a one-year contract extension.
Continuing to rehab: Tyler Bleyendaal (neck), Chris Farrell (knee), Tommy O’Donnell (shoulder), Stephen Archer (pec).
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