The 23-year old midfielder/defender missed the 2010 World Cup with a pelvic injury, which also kept him out of action for most of the 2010/11 Championship season, but is back in the Socceroos fold as they push on with their 2014 qualification attempt.
Despite aggravating the injury when on duty with Australia last month, Williams will travel to Thailand and Oman for this weekend's qualifiers and Mowbray is ok with him again representing his country.
"It is a little bit frustrating, but he's talented enough to be an international footballer and we have to trust the people with his international team that when he goes away, they also have his long-term career in mind," he told the club's official website.
"In an ideal world this break would be great for Rhys to put his feet up and continue with his strengthening programme on his body, which he does just about every day.
"The problem is that on Sunday he flew 27 hours to Australia and then 10 days later he'll be on an aeroplane for 27 hours coming back.
"Hopefully he won't be too stiff or uncomfortable to play the following day. Last time he missed the game after coming back, so we'll see how he is on the back of this trip."
But Mowbray is hoping Williams is only selected in one of the two Socceroos' fixtures so he can be fighting fit for club action when Boro host Blackpool on November 19.
"Let's hope he only has to play in one game," added Mowbray. "I'd like to think that if they get the point they need in the first one, he won't play the second.
"Being an Englishman, when the European Championships and World Cups come along I'm patriotic and desperate for them to win every game and you just can't flick it on and off.
"They have to have experience because the only way you win tournaments is by exposing players to international football.
"You can't sit as a club manager and think, 'Don't take any of my players' and then when the World Cup comes along want them to score the winning goal in the final and become £50m assets for your club.
"The manager picks his best team and rightly so because they have to qualify for tournaments. But you hope there's some common sense.
"The Australian medical staff and manager know about Rhys's condition and we hope they respect that when they pick the team."