The EC135 helicopter pilot was forced to manoeuvre to the right during the incident over Perthshire on 25 March.
The pilot was returning to base at Perth Airport after dropping off a patient in Glasgow.
A UK Airprox Board (UKAB) report said that the two aircraft came within 200m of each other.
The report said that the motor-glider had been invisible to the pilot due to being obscured by the windscreen pillar.
The pilot of the glider has not been traced.
The report noted that "flight crew situational awareness" was assessed as "ineffective" because there was no information available to the pilot to warn him about the motor-glider.
It said that as the pilot was operating in Class G or uncontrolled airspace without a collision warning system.
As a consequence "see and avoid" was his "only mitigation against mid-air collision".
The report said: "The fact that he was conducting his arrival checks had understandably reduced his and his crewman's capacity for robust and effective look-out.
"That being said, although it was a late sighting, he did see the other aircraft in time to take avoiding action, albeit achieving less separation than would be desirable."
The charity leases the EC135 helicopter and pilots from Babcock Mission Critical Services (Onshore) Ltd.
Scotland's Charity Air Ambulance chief executive David Craig said: "We are currently reviewing the report and the observations and recommendations contained within it.
"I am meeting with our aviation providers Babcock Mission Critical Services (Onshore) Ltd. later this week to determine what steps, if any, we should be taking in response to this incident and the report findings."
Scotland's Charity Air Ambulance had to take evasive action to avoid a collision with a glider, a report has revealed.