The release of the prisoners on Tuesday was made possible through Qatari mediation.
Shaikh Hamad bin Abd Allah Al Thani, a Minister at Qatar's al-Diwan al-Amiri, and a number of Red Cross officials will escort the prisoners as they head to the Moroccan city of Aghadir aboard a Qatari plane.
Secretary General of Polisario Front Muhammad Abd al-Aziz said releasing the Moroccan prisoners was a goodwill gesture in an attempt to reach an agreement on the Western Sahara conflict.
Western Sahara, a former Spanish Colony, was annexed by Morocco in 1975, prompting a long war with the Polisario who are fighting for the independence of the territory.
The territory itself is phosphate-rich and is believed to have oil deposits.
UN peacekeepers arrived in Western Sahara in 1991, but with their mission having already cost more than $500 million, some countries want to pull out the troops.
Under the latest plan, crafted by UN envoy and former US secretary of state James Baker, Western Sahara would have autonomy during a five-year transition period followed by a referendum on sovereignty.