Sources within the Long Branch school system indicate the employees thought they were "horsing around" with the Gregory Elementary School students during the incident last Thursday.
All of the children involved are younger than 10 years old.
Long Branch Superintendent Michael Salvatore, who reported the incident to police and the Monmouth County Prosecutor, said there was no indication of physical or sexual assault.
"Regardless of their intent, it was a stupid decision they made," said Salvatore.
The Monmouth County Prosecutor's office said Monday it continues to investigate the allegations and confirmed Salvatore's statement that there was no indication of any "inappropriate sexual action."
No charges have been filed at this time.
The boys, from two different classrooms, went to use the restroom and found the workers there, according to Salvatore.
Procedure calls for a facility to be closed whenever work is being done inside, he added.
Salvatore said it was his understanding that yellow caution tape may have been used on the boys.
He added that he was not told they appeared distressed, but the children did report the incident to the school's principal, who then contacted the central office.
The two maintenance employees, apparently including a plumber, had been sent to the school to make some repairs in the bathroom.
Parents on Monday expressed disgust at what was alleged.
"It's just devastating what occurs, or what can occur, when we drop our kids off," said Milce Reynoso.
Both workers were sent home early and have since been suspended from their jobs.
One source who talked with the employees told NBC News that the workers are "devastated" by how this turned out and that at no point was it intended as anything more than just having fun.