The Moroccan Foreign Ministry said in a statement issued on Sunday that Boutefliqa's stance, which comes prior to the Arab Maghreb Union's summit due to be held in Tripoli, Libya, later this week, was contradictory to the two countries' recent agreements.
Boutefliqa on Sunday congratulated the Polisario Front, on the 32nd anniversary of its creation, and pledged Algiers' continued support for the movement's bid for the independence of Western Sahara from Morocco.
Leader of the front, Mohamed Abdelaziz, on Saturday warned of a resumption of the fighting that ended with a ceasefire in 1991.
Morocco regained Western Sahara after former colonial ruler Spain pulled out of the large, phosphate-rich desert territory in 1975 and considers the area as part and parcel of the kingdom's sovereignty.
The Polisario Front took up arms for independence the following year.
A United Nations peacekeeping mission has been deployed in the region since the 1991 ceasefire but international efforts to resolve the conflict between the two sides have failed.
Last month the UN Security Council extended the mission by six months and called on both sides to help clear up the fate of people who have vanished during the fighting.