"The government of HM the king expresses its strong protest against this surprising attitude, while all assurances were given previously," an official statement by the Moroccan government said.
"The kingdom of Morocco demands ... appropriate explanations from the Libyan authorities on this unfriendly behaviour towards the feelings of the Moroccan people."
The Polisario is a political and military group fighting for the separation of Western Sahara from Morocco.
It was set up in 1973 and established itself as the sole representative of the nomadic Saharan, or Sahrawi people, fighting a war with Morocco.
Polisario staged a guerrilla war in 1976, which ended in a 1991 UN-brokered ceasefire.
Morocco has recently proposed providing the territories with a large amount of autonomy within the framework of a united and sovereign Morocco.
Rabat insists that its autonomy plan offers "the only realistic solution", but the Polisario Front rejects the proposals and has called for a referendum on self-determination.