The 38-year-old right-hander sustained a quadriceps tear during the opening game of the Hallyburton Johnstone Shield season.
She picked up the injury while fielding and has returned to Auckland, where she lives.
Scans revealed a tear that will require three months of rehabilitation.
The recovery timeline means Bates will be unavailable for the Otago Sparks for the remainder of the domestic home summer and for the White Ferns’ series against Zimbabwe in February, which includes three ODIs in Dunedin.
Bates has turned her attention to being available for the T20 and ODI series against South Africa in March.
"I’m gutted to be missing out this summer," Bates said in a statement.
"I was really looking forward to another season with the Sparks, especially the Super Smash.
"I’m determined to get back on the field with the White Ferns in March, so that’ll be my focus for now."
The Super Smash gets under way on Boxing Day.
The Sparks’ opening game is against Canterbury in Alexandra on December 28.
Bates’ absence will be sorely felt by the Sparks.
Last season, they reached the final of both the Super Smash and the Hallyburton Johnstone Shield, winning the latter in dramatic fashion.
But they have been unable to rediscover that form this season, and Bates is a proven match-winner.
The right-hander has played 107 T20s for Otago and scored 3518 runs at an average of 38.65.
Two of her six career hundreds in the format have been for the Sparks.
Bates has not bowled a lot in recent years, but she has a good T20 record for Otago. She has nabbed 62 wickets at an average of 24.06.
