Leeds United defender Liam Cooper has been called up as a replacement.
West Brom's James Morrison is also a doubt for Wednesday's friendly with Canada after missing his side's win over Arsenal.
Midfielder Morrison could still make the World Cup qualifier at Hampden against Slovenia on 26 March.
West Brom manager Tony Pulis was quoted as saying Phillips would withdraw from the squad with a hamstring strain.
Phillips, 26, had returned to the squad for the first time since last summer's friendlies against Italy and France but has missed West Brom's past three matches.
Hanley was given his first start by Newcastle United in nine games in a 0-0 draw away to Birmingham City, but McArthur was not in the Crystal Palace squad for their win over Watford on Saturday.
Cooper, 25, received his first international call-up for the 1-0 friendly win over Denmark last March but has yet to win his first cap.
Scotland head coach Gordon Strachan has arranged the friendly in Edinburgh as a warm-up for the match against Slovenia.
His side sit fifth in Group F after picking up only four points from their opening four games.
A continuing worry for Strachan is the lack of starts for his potential strikers.
Steven Fletcher was a late substitute for Sheffield Wednesday as Scotland team-mate Jordan Rhodes was again a preferred starter in Friday's 2-0 defeat by Reading.
Steven Naismith was a substitute again for Norwich City but played 60 minutes of the 2-0 win over Barnsley after replacing the injured Wes Hoolahan.
Chris Martin was an unused substitute for Fulham's 3-1 win over Wolves.
Meanwhile, Ikechi Anya, who is favourite to fill the troublesome right-back position, was left on the bench for Derby County's 2-2 draw with Nottingham Forest.
Stoke City right-back Phil Bardsley, who was overlooked again by Strachan, played 90 minutes of Stoke City's 2-1 defeat by Chelsea before being sent off in stoppage time.
Fellow right-back Steven Whittaker was given a rare start this season by Norwich - only his 14th appearance this term - but is also not in the Scotland squad.
Matt Phillips, James McArthur and Grant Hanley will miss Scotland's double header with Canada and Slovenia after withdrawing from the Scotland squad.