The work began yesterday after firefighters gave the all-clear for staff from the school's conservation department to enter the building after Friday's fire.
The conservators are operating a triage system, marking works most in need of urgent attention for a company of specialist removers to retrieve.
Water-damaged textiles and items that will perish if they are not given immediate attention are likely to be among the first objects to be brought out, followed by student artwork destined for this year's degree show.
The art school is to work with a number of organisations with expertise in the field, and the operation to remove artworks is expected to take several days.
The fire broke out around 12.30pm on Friday as final-year students worked on completing their entries for the end of year degree show.
Several people had to be led to safety, but no-one was hurt.
The fire completely destroyed the school's west wing library, but fire crews managed to preserve 90% of the building and 70% of its contents including the museum and lecture theatre.
Senior School staff are also working on plans to enable 600 final year students to complete their work and are considering postponing the start of the degree show, scheduled for mid-June.
Around 400 fire-fighters battled to bring the fire under control at the height of the incident.
Fire crews were still at the scene yesterday to dampen hot spots and try to dig out artworks buried by collapsed internal walls.
An investigation is trying to establish the cause of the blaze, though initial indications are that a projector overheated and lit nearby combustible materials.
Professor Tom Inns, Director of the GSA, said: "The first priority is to retrieve any of our archive and collections in need of immediate conservation, followed by the student work which will where necessary be given over to experts for conservation work to be undertaken. Other items will then be systematically retrieved."
He again praised Scottish Fire and Rescue Service (SFRS) crews who were sent to each floor to create a barrier and prevent the fire from spreading.
He said: "The SFRS did not simply go the extra mile, but a marathon in their efforts to ensure that as much of the Mackintosh Building and student work as possible was protected.
"We have been overwhelmed by the number of messages of support from the local community in Glasgow and friends across the world, and the generosity of individuals and organisations in offering expert assistance to help us in these difficult times."
Fire service Assistant Chief Officer David Goodhew said: "The professionalism of the crews was absolutely outstanding."
He said the building's age, its construction materials and the complexity of the structure all made it an extremely challenging fire, which took about six or seven hours to truly get under control.
Community Safety Minister Roseanna Cunningham added her praise for fire crews on a visit to Cowcaddens fire station yesterday.