It is claimed that there is 'too much variation' in the system and excluding a child from a school should be a last resort.
Around 40 children a day were expelled in 2016-17.
Transforming Lives for Good (TLG) helps churches support struggling and vulnerable children. Speaking on Premier's News Hour Its education director, Scott Halligan welcomed the findings.
"It's clearly a very good thing," he said. "It's a step in the right direction - we know that many of the young people that are excluded from school are often forgotten about."
Halligan believes churches have a role to play in supporting children in their communities who are struggling at school.
He said:"We exist at TLG to reintegrate students back into mainstream school - one of our mantras is the verse Jeremiah 29:11.
"We aim to enable the local church to bring hope and a future to struggling families.
"We really believe that can happen if young people come to us and we can work with them early enough, we can get them back into school.
"We can build them up and give them coping strategies.
"It tends to take us about two-terms working quite intensively with students for them to integrate back into mainstream education and not only to survive but to flourish."
The report by ex-education minister Edward Timpson makes 30 recommendations which the government says it'll adopt.
Education Secretary Damian Hinds said: "Every child deserves an education that fosters ambition and provides the knowledge and skills they need to make the most of their potential. That must include children at risk of exclusion or those that have been expelled.
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