Labour MP Lisa Nandy said medical evidence suggested the practice of X-raying young people was unethical and potentially dangerous.
And Education Secretary Michael Gove said there were "causes for concern".
The practice of X-raying young asylum seekers was reintroduced in March 2012 by the UKBA to establish a young person's age.
It has been condemned by the former Children's Commissioner for England, Sir Al Aynsley-Green, as "scandalous".
Addressing a committee of MPs, Mr Gove said: "We need to be clear that this is a proportionate, wise intervention in order to ensure that we can keep our borders safe.
"I am concerned obviously to ensure that we do not have people exploiting the generosity of this country, but I'm also clear that we should ensure that the dignity of individuals and in particular the rights of children are respected too."
Mr Gove said he had raised some concerns with the Home Office and the UKBA, but had not yet had a response.