According to the Telegraph, Sheila Jones, head, St Joseph's Roman Catholic primary in Devizes made some of the children lie face down in the prayer room while she pretended to ring God on her mobile phone.
Tammy Brimble's son Cyrus, 11, was one of those who allegedly received the "I'm phoning God about you" punishment at the school.
She said: "I didn't find out about it will we got home. Cyrus was very quiet and I could tell something was bothering him.
"When he told me what had happened to him and three other boys, I was upset but I wanted to find out why she did it.
"I don't think what she did was appropriate at all.We are not Roman Catholics but it was still distressing for my child for her to call on God like that."
Ofsted has reportedly asked Wiltshire Council's safeguarding panel to investigate the parents' complaints.
In a letter to parents, the schools' watchdog said: "Ofsted has shared your concerns with the local authority so they can progress these safeguarding concerns as they consider appropriate."
The school, which was reportedly rated as "needing improvements" at its last Ofsted review, is due to receive inspectors for a fresh assessment within a few days.
Colette Culligan, chairman of the governors, said: "We are aware of an allegation against one of the teaching staff.
"In order to follow due process, all enquiries regarding this issue need to be directed to Wiltshire Council.
"This is to ensure that any investigation currently being conducted is not unduly influenced."
A Wiltshire Council spokesman said: "Once we have received the letter from Ofsted we will look into any concerns raised."
