Austin, 28, qualifies for England through his grandmother.
Hughes has a groin injury, but hopes to be fit to take part in Great Britain’s tour of New Zealand and Papua New Guinea, which follows the Nines event.
England’s men’s and women’s teams will play their first matches of the tournament in Sydney on 18 October.
The women’s team will also be forced into a squad change, as Leeds Rhinos forward Shannon Lacey sustained a head injury in their Super League semi-final win over St Helens last week – which will also rule her out of Friday’s Grand Final against Castleford.
Her replacement is yet to be named.