The Ulster wing suffered what his province have described as "significant lateral ligament damage" to his right knee during Saturday night's Heineken Cup home defeat against Northampton.
Bowe was carried off late in the second half at Ravenhill following a lengthy stoppage, and Ulster supporters chanted his name as he was taken away.
In a statement issued on Sunday, Ulster said: "An initial scan this morning revealed that he has sustained significant lateral ligament damage to his right knee.
"He will undergo surgery later this week to repair the damage.
"At this stage, it is not possible to put a timescale on how long his recovery period will be.
"A further update on this will be issued following the surgery, when the full extent of the injury will be known."
Ireland kick off this season's Six Nations tournament against defending champion Wales in Cardiff on February 2.
Bowe, whose prospects of touring Australia with the British and Irish Lions could conceivably be jeopardised by his current injury, is an integral part of Ireland coach Declan Kidney's plans.
The 28-year-old former Ospreys player has scored 26 tries in 51 Tests, and he is rated among the deadliest finishers in European rugby.
He started all three Tests for the 2009 Lions in South Africa, the final Test at outside centre when the Lions won in Johannesburg.
Ireland's season has been badly-affected by injuries, with Brian O'Driscoll, Paul
O'Connell, Rory Best, Stephen Ferris and Sean O'Brien all missing the entire autumn series last month.
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