"Armenia has launched an outrageous policy of massive illegal settlement of the Armenian population into the occupied Azerbaijani territories, which is a blatant violation of the international law," he said.
The conflict has forced more than 1 million Azerbaijani people to become refugees, Aliyev said.
"The situation deteriorates with the use of these territories for drug trafficking, arms transfers, harboring terrorists, illegal economic activities and smuggling."
Azerbaijan has asked for U.N. participation in returning the refugees to their Azerbaijani homes. The two countries have long been in contention, the Azerbaijani a Muslim nation historically allied with Iran and Turkey, and the Armenians a Christian people who accuse the Turks of genocide in the early 20th century.
Aliyev criticized the U.N Security Council for having a "passive and silent attitude" on the migration issue.
"We expect more responsive strategy by the United Nations in relation to the situation of a forgotten humanitarian crisis in Azerbaijan," Aliyev said.