Cassia County School District officials said Monday that they filed a formal complaint against Declo Elementary School fourth-grade teacher Summer Larsen.
Some parents and administrators said the face-marking punishments given to six students in Larsen's class were inappropriate and left the children feeling shamed.
The Idaho State Department of Education's Professional Standards Commission, which has the power to suspend or revoke teaching licenses, will examine the case, the Twin Falls Times-News reported.
The students were allowed to choose their own incentive to meet the reading goal. But instead of a reward, the class chose a punishment: Students who failed to meet the goal could either stay inside at recess until it was met, or have their faces written on by classmates who met the goals.
Nine students didn't meet the goals, the Times-News reported. Three chose to skip recess, and the other six opted to have their faces marked.
The ink was difficult to wash off, and some of the children said they felt humiliated - especially when they had to ride the bus home.
One 10-year-old came home in tears after his entire face, including his eyelids, had been scribbled on with green, red and purple markers.
"The investigation on this is also ongoing in the district," said Cassia County School District Superintendent Galen Smyer, declining to give specifics on the complaint other than to say it's a "personnel issue."
He said Larsen remains employed with the district but he wouldn't confirm whether she was placed on administrative leave.
Efforts to contact Larsen were unsuccessful.