Morocco's ambassador to the United Nations, Muhammad Bennuna, criticised Annan in a letter to the Security Council for urging his country to become "actively engaged in implementing" a settlement proposed by former US Secretary of State James Baker.
Rabat has rejected the Baker plan, backed on 30 July by the Security Council, saying its implementation would pose "major risks" for security and stability in the region.
Under the resolution, mineral-rich Western Sahara, a former Spanish colony annexed by Morocco in 1975, would have a large degree of autonomy during a five-year transition period, followed by a referendum to decide on the territory's sovereignty.
Morocco views the plan as a stepping stone to Western Sahara's independence, which it opposes.
The Baker plan was accepted by the Polisario Front, an armed movement in Western Sahara, which is backed by Morocco's eastern neighbour Algeria and has been seeking independence from Morocco for the last 28 years.
It was "mistaken to deduce from Resolution 1495 that a pure and simple signature is expected from Morocco"
Moroccan ambassador to UN
The Moroccan letter, published by the official news agency MAP on Wednesday, said Annan's office had "deviated from its neutrality and its objectivity by deliberately giving an erroneous interpretation of Resolution 1495” adopted on 30 July.
Annan ignored "the content of the text, the preparatory work leading to its adoption ... especially the statements made by the members of the Security Council” after the 30 July vote, Bennuna wrote.
The Security Council conditioned its support of the Baker plan on "the approval of the parties", he wrote.
It was "mistaken to deduce from Resolution 1495 that a pure and simple signature is expected from Morocco" of the Baker plan or that Morocco should take "concrete steps" to implement it, the letter added.
"All the members of the Council clearly rejected the option of imposing the plan," Bennuna wrote.
Annan on Monday recommended the renewal for three months of the mandate of the UN Mission for the Referendum in Western Sahara (MINURSO), which is due to expire on 31 October.
The United Nations has failed since 1991 to organise a referendum on self-determination in Western Sahara as demanded by Polisario, because of sharp differences over which groups should be allowed to take part in the plebiscite.