The Santa Monica school board told the L.A. Times it just learned about the 2006 complaint this week after Beltran's arrest.
The school board president blames a breakdown in communication and says the principal who reported the 2006 allegations is no longer with the district.
The veteran teacher who taught English as a second language at Lincoln Middle School has been charged with eight counts of committing a lewd act on a child and three counts each of continuous sexual abuse and sexual penetration of a foreign object on a child under 14.
Authorities say that the lewd acts took place during school hours.