"We are not turning any children away from the school," Father Ian Ranson told The Age.
Earlier the paper had reported that the school wrote to the Benic family on Wednesday advising them that their children had been enrolled at another school from Monday, without the family's knowledge.
Anti-discrimination consultant Julie Phillips, who is advising the family, said she was concerned the children had been removed from the school because the elder child, Stefan, 12, had a severe language disorder.
Ms Phillips said the school's decision to let the children return on Monday was pleasing. "Stefan is looking forward to rejoining his peers in the regular classroom on Monday," she said.
Fr Ranson said he wrote the letter to the Benics informing them of a move because the relationship between the family and school was at "crisis point" after years of tension.
He said the school had not tried to remove the children because of Stefan's severe language disorder. "It's not because of his disability, it's not the individual. It's the family and the school," he said.
Fr Ranson said there had been "dissatisfaction from the parents for many, many years despite many meetings".
He defended the school's decision to try to move the family to another primary school within the parish without consulting the family, describing it as "the only option".
Following Friday's report in The Age, the school arranged a meeting between it, the family, Ms Phillips, and the Catholic Education Office.
David Huggins, from the Catholic Education Office, supported the school's handling of the case.
"There has been a long process of conciliation, mediation and collaboration," he said, adding that the office had been aware of the case for many years.
School retreats on moving of siblings (The Age, 21/5/07)
LINKS (not necessarily endorsed by Church Resources)
St Martin de Porres Primary School, Laverton
Parish priest sends students to state school (CathNews, 18/5/07)
21 May 2007