Baker, deeply frustrated by his inability to end the impasse during his seven year tenure, told UN Secretary General Kofi Annan of his intention to resign several days ago, but the Security Council was not formally notified until Friday, UN diplomats said.
Annan named Baker as his personal troubleshooter on the contentious dispute in March 1997.
The fate of the vast northwest African territory of about 260,000 people, rich in phosphates and also believed to have offshore oil deposits, has been contested since Morocco
seized it in 1975, immediately after it won independence from colonial power Spain.
The UN has been involved in efforts to resolve the dispute for 13 years.
"This is a serious setback to the UN effort for resolving the West Sahara issue," said Ahmad Boukhari, a representative of the Polisario Front independence movement.
"It's a great loss for
the peace effort, but
he has left behind as
his legacy a clear
peace plan based on
for the people of
Polisario Front representative
"It's a great loss for the peace effort, but he has left behind as his legacy a clear peace plan based on self-determination for the people of Western Sahara," Boukhari said.
Morocco "worked closely with Mr Baker, making us better aware of what we could accept and what were our red lines", Rabat's ambassador to the UN, Muhammad Binnouna, told Reuters.
"We thank him for all his efforts and especially for his patience."
Baker's latest compromise proposal was to make Western Sahara a semi-autonomous part of Morocco for four to five years, followed by a referendum letting residents choose either independence, continued semi-autonomy or integration with Morocco.
The Polisario Front and its principal backer, Algeria, welcomed the plan, but Morocco announced on 9 April that it could accept only "autonomy within the framework of Moroccan sovereignty" for Western Sahara.