Nguyen Thi Thuan, a nurse at Huong Hoa District General Hospital in Quang Tri province, was charged with "accidentally causing human death due to a breach of professional or administrative regulations," provincial police spokesman Nguyen Van Loi said.
After her arrest last week, Ms Thuan admitted injecting Esmeron, a medicine commonly used as a general anaesthetic.
The charge carries a maximum penalty of 12 years in jail.
The deaths occurred in July last year. Ms Thuan was arrested briefly at the time but was released after she insisted that she administered the vaccine correctly. The families of the children did not give permission for autopsies to be carried out.
The Ministry of Health suspended use of the vaccine for five months in the wake of the children's deaths.