"Women are a special case for very good, evidenced reasons. Firstly, many more women who go to prison have themselves been victims. They've often been abused or in violent partnerships," Hughes said on air of BBC Radio 5.
He added that it was his belief that women tend to leave behind family responsibilities, unlike men.
Hughes stressed that he was primarily referring to women sentenced for non-violent crimes.
"There are some women who do terrible things and deserve to be locked up for a very long time. My concern is for those who are not a danger to society, who have become caught by a system which then does not help them out of it," Hughes said.
The 2013 research by the UK Prison Reform Trust (PRT) suggests that almost half of women released from prison are re-convicted within a year.
No job, no hope – lack of employment support is undermining the rehabilitation of women offenders @PRTuk's new report http://t.co/XJzDFwApFB
— Prison Reform Trust (@PRTuk) 29 января 2015
There are currently about 3,800 women imprisoned in England and Wales, according to UK Ministry of Justice data.