The girl's mother, Jade Masters-Ownbey, told the Canon City Daily Record on Wednesday that the school district did a "great job" protecting her daughter from repeated harassment from the boy.
First-grader Hunter Yelton was initially given a two-day suspension, with a sexual harassment infraction on his discipline record.
The boy's mother, Jennifer Saunders, says the punishment was too harsh.
"He is 6 years old, and that is absolutely ridiculous for him to have 'sexual harassment' on his record, even it is (only on the district's) record," she said.
The school district has done an about face.
"The parents of the student and the principal met this morning. One of the outcomes of the conference was to change the category of the disciplinary offense from "sexual harassment" to "misconduct". The student has returned to school," Cañon City Schools Superintendent Robin Gooldy told ABC News in a statement.
But Masters-Ownbey says the kissing was "not once, but over and over." She said she hoped people would not "start bashing the school that is doing a great job protecting my child from what is sexual harassment."
School officials insist the boy was repeatedly warned and that the punishment was warranted.
Lincoln Elementary School Principal Tammy DeWolfe said the school would "never suspend a student for one minor little violation."
No criminal charges have been brought against the boy.
Masters-Ownbey stated her daughter's older brother has felt like he needed to protect her at school.
"In elementary school, when a boy kisses a girl, the usual response of their peers is 'ewwww,'" she stated. "So why do the other kids rush to tell? Because they've seen it over and over, they've seen him repeatedly get in trouble for it, they've seen the girl repeatedly tell him to stop, they know it's wrong."
(The Associated Press contributed to this report)