Ahmed Boukhari, the Polisario Front's representative to the United Nations, has died following a battle with cancer, diplomats told AFP on Wednesday.
Boukhari, whose represented the group seeking independence for Western Sahara, died on Tuesday, one diplomat said on condition of anonymity.
The day before his death, he had written to the UN Security Council rebutting Moroccan charges that Polisario fighters launched incursions in a buffer zone of Western Sahara where a UN mission is monitoring a ceasefire.
Morocco and the Algerian-backed Polisario fought for control of Western Sahara from 1975 to 1991.
On Sunday, Morocco told the Security Council that Polisario Front fighters had entered the northeastern town of Mahbes in violation of the buffer zone - and threatened a firm response.
The United Nations said its MINURSO mission had not observed any such movement of fighters.
The Moroccan threats came as the Security Council is discussing a new mandate for MINURSO, which has been monitoring the truce since 1991.
The UN is also seeking to relaunch negotiations on a settlement that have been stalled since 2012.
Morocco maintains that settlement negotiations should focus on its proposal for autonomy for Western Sahara, and rejects the Polisario's insistence on an independence referendum.