The prosecutors decided to file charges even though Sweden's National Board of Health and Welfare cleared the doctor of any wrong doing in 2009, the Swedish news agency TT reported Wednesday.
The attorney for the accused physician said his client was devastated by the news that she is being charged.
The physician is accused of speeding up the baby's death by administering a high dose of an anesthetic in combination with morphine, TT reported.
The 3-month-old female infant was born 15 weeks premature with serious brain damage.
Medical colleagues and the unions have criticized law enforcement authorities for their handling of the case.