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Lentjes has damaged his shoulder and a scan last week confirmed the only way to fix it was to go under the knife.
Otago coach Cory Brown said Lentjes (26) had been struggling with the shoulder and it had been agreed the best option was to have an operation and start the long road back to full fitness.
The scan had shown structural damage to the shoulder and the only option was an operation.
He is scheduled to go under the knife in the middle of next week and it is expected his recovery will take about six months.
Brown said Lentjes thought he had been struggling of late because of the shoulder and something had to be done.
Brown felt Lentjes, who captained Otago in its game against Northland last Wednesday, had been playing very well and got through a lot of work this season, especially for a player who was favouring a shoulder.
It is tough luck for the Taieri flanker who was also hampered by injury in this season’s Super Rugby campaign for the Highlanders.
He started the season as the Highlanders’ only fit openside flanker but was struck down by a dislocated elbow in just the second game of the season in early March.
He did not get back on the field for three months, although he came off the bench for the side in its win over the British and Irish Lions team in mid-June.
With six months on the sideline, Lentjes is unlikely to be ready for the Highlanders for the start of next season.
The side has signed up Dillon Hunt and Dan Pryor for next year to play openside flanker but both have had injury issues this season.
Pryor did not play at all for the Highlanders this season, due to a knee injury, although he is back playing for Northland. Hunt has missed the past two weeks because of concussion.