Some 98.6 percent of votes cast in Sunday's poll approved a constitution declaring the Armenian-backed Nagorny Karabakh an independent state.
"In the end it will have negative rather than positive consequences.
Such a referendum does not contribute to a peaceful resolution," Azerbaijan's Foreign Minister Elmar Mammadyarov told journalists on Monday.
"The passing of a legal resolution would need the participation of absolutely all citizens, the citizens of Azerbaijan. Without their participation it is frivolous," he said.
Nagorny Karabakh first declared itself independent in 1991, precipitating a full-blown war between former fellow Soviet republics Armenia and Azerbaijan, which claimed some 25,000 lives before ending with a ceasefire in 1994.
Years of negotiations have failed to resolve the dispute between Azerbaijan and the Armenian-backed Nagorny Karabakh separatists.
Mammadyarov suggested that the referendum indicated that Armenia was not negotiating in good faith.
"On the one hand they say 'yes' we agree that negotiations be brought forward, and on the other hand they hold a constitutional referendum. It's a joke, a farce, nobody will accept it," he said.
The chairman of the Organization for Security and Cooperation in Europe, a key player in the peace negotiations, on Monday called the referendum "counter-productive."
The European Union said it "recognizes neither the 'referendum' nor its outcome."
Armenian Foreign Minister Vardan Oskanyan said the vote would not impede the peace process.
"The referendum will not hinder the continuation of the negotiating process, as the basis for the peaceful resolution lies in the right of the people of Nagorny Karabakh to self-determination," he told Russia's RIA Novosti news agency ahead of the vote.
- Baku Today
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