The disappointing early exit from the new event for the 24-year-old from Oban was announced by his management company, Bounce Sport.
"Unfortunately, @robert1lefty has had to withdraw from #AXAScottishChamps due to a niggle around his hip/back which has been causing discomfort these last couple of weeks," said a post on Twitter.
"Under current Covid-19 restrictions, European Tour physios are only able to give each player 15 minutes per day at present.
"That means he has had to withdraw to receive more intense treatment to enable a return to full fitness and be ready to play in Cyprus the week after next."
MacIntyre had opened with a six-over-par 78 in the company of Lee Westwood and Aaron Rai after getting off to a poor start and not having a single birdie on his card.
The young Scot has had his fair share of frustration since being crowned as European Tour Rookie of the Year in Dubai last November.
He was forced to delay the start of his 2020 campaign due to a niggling wrist injury and hasn't quite managed to fire on all cylinders yet this year.
That said, he made the cut in both the US PGA Championship and US Open in his first two majors on American soil.Ewen Ferguson, Scott Jamieson and Marc Warren are the leading Scots heading into the second round in St Andrews.
They all opened with five-under 67s to sit joint-eight behind Adrian Otaegui after the Spaniard carded a sensational 62.