The Annual Report by Her Majesty's Chief Inspector of Education, Children's Services and Skills 2016/17 found that a third of independent Christian schools are inadequate or need improvement.
Clive Ireson, director of the Association of Christian Teachers, told Premier the schools should be given some time to adjust because it's been two years since they've had to switch to Ofsted's rules.
Prior to 2015, the schools were inspected by the Bridge Schools Inspectorate.
Ireson said: "They've got new standards.
"That's not to say they don't need to be good.
"We're expecting something different from them and I'm sure they'll get there in the fullness of time."
Amanda Spielman, the chief executive of Ofsted said some faiths schools "seek to isolate young people from the mainstream, do not prepare them for life in Britain or, worse, and actively undermine fundamental British values".
Ireson explained that Christian schools must learn to keep their "faith flavour" while still meeting requirements.
"The two shouldn't be in conflict; we need to make sure they're not," he said.
"Teachers should be able to express their faith in these schools and that's why their parents have chosen to send them there.
"But they need to make sure the children aren't following an agenda that doesn't fit the community, because we need community cohesion and we need to prevent radicalisation."
Ireson admitted that he's not sure that Ofsted always understands independent faith schools.
Out of the 99 independent schools inspected, 14 per cent were outstanding, 52 per cent were good, 15 per cent needed improvement and 18 per cent were inadequate.
Ireson told Premier the report is slightly weighted because not all of the schools have been inspected yet.
"The results look worse than they are", he said.
"They've inspected a large proportion of the schools and they're going to inspect the rest by August 2018.
"I'd like to see some of these schools [undergo] their second inspection and I think we'll see a turnaround in some of the results."
Listen to Clive Ireson speaking with Premier's Tola Mbakwe here:
