Team Scotland issued a statement on Monday saying the 21-year-old Paisley-born sportsman had left the competition.
No reason was given for his departure but it is understood that he picked up an injury.
Allan won the Scottish National Senior Championships last year and came third in the European Athletics U23 Championships.
He was due to compete at Hampden.
His brother David is also a high jump competitor in the team.
A Team Scotland spokeswoman said: "Team Scotland can confirm that high jumper Allan Smith has withdrawn from the Glasgow 2014 Commonwealth Games."