Hughes surprised many when he pulled off the signing of Brazil goalkeeper Julio Cesar from Inter Milan this week.
The 32-year-old will now become first choice at Loftus Road, relegating Green after unconvincing displays in his first two games for the club.
Green, who signed on a free transfer from West Ham this summer, is likely to fear his for his international career if he cannot wrest the number one jersey back from Cesar.
"In the future if any of my keepers came to me and said they felt their future lay elsewhere then we can have a conversation about that and make a decision that benefited everyone," Hughes said.
Green, who has represented England 12 times, may well feel aggrieved that he is second choice a few weeks after arriving to replace Paddy Kenny, who left for Leeds.
But his performances in the 5-0 defeat to Swansea and 1-1 draw against Norwich were way below par.
Hughes insists that Green fully understands the decision to sign Cesar and claims it was always his intention to bring in another goalkeeper before the transfer window shut.
"It's important that Rob doesn't feel that this was a knee-jerk reaction," Hughes said.
"I was told there was a possibility that Julio Cesar would look favourably on coming to Queens Park Rangers so we tried to pursue it.
"We managed it and that will obviously have some impact on Rob because there will be competition for him.
"He understands that but he has been a top keeper for a long time and I'm sure he will be ready for that challenge. Whoever is out of the team knows he will have to work hard to get back in the side.
"Rob fully understands the thinking behind what we have done although it might impact him throughout the season."
Green will at least start Saturday's game against Manchester City because Cesar has not received international clearance to play.
One man who is available is Esteban Granero, who signed from Real Madrid on Thursday night.
Hughes was happy to snap up the 25-year-old midfielder and revealed the club were close to signing the player in January.
"He wanted to come in January but Real Madrid got an injury a couple of days before we were supposed to conclude it so they didn't let him out," Hughes said.
"He's going to be a good player for us. He has been brought up at a top club since he was nine and having been at Real Madrid has values and standards."