CRS Regional Commander Sean McCarry said the car had deteriorated to less than half of its original structure, with much of what remained embedded in mud and soil.
“Considering the amount of concern and public interest, it was decided for safety reasons that we should remove the visible portions of the vehicle despite their poor condition,” he said.
McCarry said further debris could potentially be removed when river conditions allow.
The material recovered during the operation was taken away for disposal.
CRS said it would continue to coordinate with the council and local representatives, and would return to the site when conditions are suitable to assess and remove any further visible remains.
Alliance councillor Nicola Parker, who was present during the removal, said the car had deteriorated significantly after spending so long in the water.
“It has been in the water for so long, that it is now paper thin and there wasn’t much to hold it together”.
She said the recovery team encountered difficulties while trying to remove the vehicle, with the main base of the car buried in the riverbed.
The vice-chair of Lisburn and Castlereagh City Council’s environment and sustainability committee added that they best possible outcome would have been to remove the car entirely but that was not possible.