Barnardo's, which runs family welfare services at the government's "child friendly" pre-departure accommodation centre, the Cedars immigration detention facility in Crawley, West Sussex, is calling on the next government to address the issue.
A report by the children's charity highlights that since the immigration returns process was changed by the coalition government in 2010, there has been a 90 per cent drop in the number of children being detained for immigration purposes, and the quality of accommodation has "radically improved".
But it says there are still areas of practice that government must improve.
Barnardo's said "family splits" when one, or both of the parents have been separated from their children for any period from a few minutes to a few days, are often being used as a way of dealing with non-compliant behaviour.
"As a child welfare organisation this concerns us, as we do not think a family split should be used for the purposes of effecting immigration enforcement," the report states.
In addition to families being separated, Barnardo's has raised concerns about families released from Cedars being placed in "substandard" accommodation, savings being confiscated from them, and pregnant women being detained.
It also wants the Home Office to change arrest procedures to make them more "child friendly", and calls for police to stop wearing protective equipment during the process, unless a risk assessment deems it necessary.
"The government has made significant improvements in the way that children and families are treated within the asylum process," Alison Worsley, Barnardo's deputy director of strategy said.
"However, there is still much work to do to improve the Family Returns Process and the wider immigration process.
"Children should never be separated from their carers for the purposes of immigration control, and every step should be taken to ensure that pregnant women are not detained for immigration purposes.
"We ask the next government to live up to its moral responsibility to some of the UK's most vulnerable children and implement Barnardo's recommendations."
The report reveals that in the first three years Cedars has been in operation, 136 families and 271 children have stayed there - 58 families with 120 children in its first year, 50 families with 90 children in the second year, and 28 families with 61 children in the third year.
The Family Returns Process was introduced by the coalition government in 2011 to deal with families that have no legal basis to remain in the UK.
It includes a family returns conference to explain options for voluntary return schemes.
If a family does not make arrangements to return voluntarily, then the Home Office makes arrangements for a "required return".
Families are given at least two weeks' notice of their departure date and are expected to self-check-in at the airport.
An "ensured return", which involves families being taken to the pre-departure accommodation at Cedars prior to being boarded on a flight, is used as a last resort if the other options fail.
The Home Office has declined to comment on the report, stating it is a matter for political parties contesting the general election.