The midfielder will require surgery on his shoulder, a procedure which will keep him sidelined for three months, and is keen to have the operation done soon to ensure he is fully fit for next season.
The injury did not stop the former Swansea man featuring off the bench in Liverpool's 3-2 win over Tottenham, and Coleman has selected him in his 23-man squad as Wales look to build on their encouraging win over Austria last month.
The Wales boss is not expecting the powers that be at Anfield to deprive him of the services of one of his key players.
He said: "(Liverpool manager) Brendan Rodgers commented that at some stage he will have to have surgery but at no time have we been told he's not available.
"If that was the case, we wouldn't pick Joe, I totally respect Brendan Rodgers and Liverpool Football Club and I think we'll always try to work with club because they aren't our players and we're only borrowing them.
"But we've not told been told anything so at the minute he's very much in the squad."
One man who has missed out is Celtic defender Adam Matthews, due to the hamstring injury he picked up in the Hoops' Champions League exit at the hands of Juventus.
Coleman sympathises with the 21-year-old, who would have been desperate to feature in next Friday's clash at Hampden Park, but has not ruled out having him available to meet Croatia in Swansea in the second game of the double-header.
"I thought Adam was outstanding against Austria and he really is developing into a fine young player, so it's disappointing," said Coleman.
"We know he's definitely out of the first game but we don't know about the second one yet, there' a bit more time for him so it's wait and see on that.
"He has an extra three or four days which with the injury could make a big difference.
"At the minute we have to think he's unavailable. It would have been a great game for him in Scotland given he's playing in Scotland with Celtic and he's in tremendous form, so it's a shame."
Tottenham winger Gareth Bale is included, with Wales hoping to see a continuation of his stunning recent form, which has delivered 11 goals in his last 10 games.
James Collins provides a welcome option at centre-half after missing the 2-1 win over the Austrians, while Leeds striker Steve Morison is another to return from injury.
But Darcy Blake has been deemed short of match fitness and is omitted.
Uncapped midfielder Jonathan Williams is promoted from the under-21 squad after scoring in their 3-0 win over Iceland and impressing with his performances for Crystal Palace.
Cardiff striker Craig Bellamy is again included after rubbishing reports of retiring from international football, while Arsenal midfielder Aaron Ramsey is back after being a late withdrawal for the game against Austria.
Wayne Hennessey is a long-term absentee as the Wolves number one continues his rehabilitation from a serious knee injury, so Boaz Myhill, Lewis Price and Owain on Williams are the three goalkeepers selected.
Wales squad for the World Cup qualifiers against Scotland and Croatia: Boaz Myhill (West Brom), Lewis Price (Crystal Palace), Owain Fon Williams (Tranmere); Ben Davies (Swansea), James Collins (West Ham), Chris Gunter (Reading), Joel Lynch (Huddersfield), Jazz Richards (Swansea), Sam Ricketts (Bolton), Ashley Williams (Swansea, captain); Joe Allen (Liverpool), Jack Collison (West Ham), Andy King (Leicester), Joe Ledley (Celtic), Aaron Ramsey (Arsenal), David Vaughan (Sunderland), Jonathan Williams (Crystal Palace), Gareth Bale (Tottenham); Craig Bellamy (Cardiff), Simon Church (Reading), Steve Morison (Leeds), Hal Robson-Kanu (Reading), Sam Vokes (Burnley).