Students were asked to fill out the forms last week. They included questions such as: "Who do you share saliva with?" and "Are you sexually active?"
New Mexico teachers are not allowed to talk to students about sex without parental consent- that way parents can opt their child out of the activity if they want.
But the biology teacher didn't ask anyone for permission when he handed out the sexual activity forms to at least freshmen and juniors.
Parents were outraged when they found out about the assignment.
"I feel really offended right now, they didn't inform us," said one parent.
"This was something that should not have occurred, and obviously we'll be taking steps to see that it doesn't occur again," said Kim Vesley from Rio Rancho School District.
School district officials say the survey was part of an unapproved class project and the incident is now under investigation.
ABC News contributed to this story.