Azerbaijan's president Ilham Aliyev has said he achieved a decades-long "Azerbaijani dream" by retaking Karabakh from Armenian separatists, as he raised his country's flag in the region's main city.

Dressed in military attire, the longtime leader flew the blue-red-green flag in Khankendi on Sunday, cementing Baku's conquest after last month's offensive.

It was the first time Aliyev had set foot in the city since it fell to Armenian separatists in the 1990s.

"We achieved what we wanted. We fulfilled the dream the Azerbaijani people have lived with for decades," Aliyev said in a victory speech, adding that his country "waited 20 years" to see Azerbaijani rule in Karabakh.

"This victory will stay in our history forever," he said triumphantly.

End of decades-long conflict

Baku published images of the longtime leader in military attire on his knees, kissing the Azerbaijani flag before it was raised on a flagpole.

It said he also visited a reservoir and an ancient fortress, as well as other towns.

"Twenty years ago, when I began to fulfil my official duties as president, I set myself a number-one task," Aliyev said.

"So that on all territories, on all lands, in all towns and villages that at the time were under occupation, the Azerbaijani flag would fly."

Azerbaijan regained full control over its territory of Karabakh last month after taking counter-terrorism actions in the area, which resulted in the surrender of illegal armed groups, ending a decades-long conflict.

Authorities have repeatedly said that they will protect the rights and ensure the security of the Armenian residents in Karabakh, in accordance with Azerbaijan's law.