Numerous appeals were filed by both Armenian and international organizations, condemning the Azerbaijani government and calling on it to desist from such activity. In 2006, Azerbaijan barred European Parliament members from investigating the claims, charging them with a "biased and hysterical approach" to the issue and stating that it would only accept a delegation if it visited Armenian-controlled territory as well.
Armenia first brought up charges against the Azerbaijani government for destroying khachkars in 1998 in the town of Julfa. Several years earlier, Armenia had supported Armenian separatists fighting for their independence in the enclave of Nagorno-Karabakh in Azerbaijan, in the Nagorno-Karabakh War. The war concluded in 1994 with a cease fire that resulted in Azerbaijan losing 14% of its territory, including those outside of Nagorno-Karabakh and the de facto but unrecognized state of the Nagorno-Karabakh Republic. Since the end of the war, enmity against Armenians in Azerbaijan has built up. According to the Archaeological Institute of America, the loss of Nagorno-Karabakh to the Armenians has "played a part in this attempt to eradicate the historical Armenian presence in Nakhchivan."
In 1998, Azerbaijan dismissed Armenia's claims that the Khachkars were being destroyed. Arpiayr Petrosyan, a member of the organization Armenian Architecture in Iran, had initially pressed the claims after having witnessed and filmed bulldozers destroying the monuments.
Reacting to the claims, the government of Iran expressed concern over the destruction of the monuments and filed a protest with the Nakhchivan Autonomous Republic's government (NAR). Hasan Zeynalov, the permanent representative of the NAR in Baku, stated that the Armenian allegation was "another dirty lie of the Armenians." The government of Azerbaijan did not respond directly to the accusations but did state that "vandalism is not in the spirit of Azerbaijan." Armenia's claims provoked international scrutiny that, according to Armenian Minister of Culture Gagik Gyurdjian, helped to temporarily stop the destruction.
Armenian archaeologists and experts on the khachkars in Nakhchivan stated that when they first visited the region in 1987, prior to the break up of the Soviet Union, the monuments had stood intact and the region itself had as many as "27,000 monasteries, churches, khachkars, tombstones" among other cultural artifacts. By 1998, the number of khachkars was said to have been reduced to 2,700.
The old Cemetery of Julfa is known to specialists to have housed as many as 10,000 of these carved khachkar headstones, up to 2,000 of which were still intact after an earlier outbreak of vandalism on the same site in 2002. Eyewitness accounts of the ongoing demolition describe an organized operation. In December 2005, Iranian Armenians documented more video evidence across the Araks river, which partially demarcates the border between Nakhchivan and Iran, stating that it showed Azeri troops had finished the destruction of the remaining khachkars by using sledgehammers and axes.
Azerbaijan's government has faced a flurry of condemnation since the charges were first revealed. When the claims were first brought up in 1998, the United Nations Educational, Scientific and Cultural Organization (UNESCO) ordered that the destruction of the monuments in Julfa cease. The complaints also brought forward similar appeals to end the activity to stop by the International Council on Monuments and Sites (ICOMOS).
In reaction to the charges brought forward by Armenia and international organizations, Azerbaijan has asserted, falsely, that Armenians had never existed in those territories. In December 2005, Zeynalov stated in a BBC interview that Armenians "never lived in Nakhchivan, which has been Azerbaijani land from time immemorial, and that's why there are no Armenian cemeteries and monuments and have never been any." Azerbaijan instead contends that the monuments were not of Armenian origin, but of Caucasian Albanian.
In regard to the destruction, according to the Azerbaijani Ambassador to the United States, Khafiz Pashayev, the videos and photographs that have surfaced do not show the identity of the people nor display what they are actually destroying. Instead, the ambassador asserts that the Armenian side started a propaganda campaign against Azerbaijan to divert attention from the alleged destruction of Azerbaijani monuments in Armenia. Azerbaijan President Ilham Aliev also denied the charges, calling them "a lie and a provocation."
Numerous non-Armenian scholars have condemned the destruction and urged the Azerbaijan government to give a more complete account. American anthropologist and associate professor of anthropology at the University of Chicago, Adam T. Smith, called the removal of the khachkars "a shameful episode in humanity's relation to its past, a deplorable act on the part of the government of Azerbaijan which requires both explanation and repair." Smith and other scholars, as well as several United States Senators, signed a letter to UNESCO and other organizations condemning Azerbaijan's government.
In the spring of 2006, a journalist from the Institute for War and Peace Reporting claimed to have visited the cemetery and wrote that it had "completely vanished." In the same year, European parliamentary members protested to the Azerbaijani government when they were barred from inspecting the cemetery. Hannes Swoboda, an Austrian socialist MEP and committee member who was denied access to the region, commented that "If they do not allow us to go, we have a clear hint that something bad has happened. If something is hidden we want to ask why. It can only be because some of the allegations are true." Doctor Charles Tannock, a conservative member of the European Parliament for Greater London, echoed those sentiments and compared the destruction to the Buddha statues destroyed by the Taliban in Bamyan, Afghanistan in 2001. He cited in a speech a British architect, Steven Sim, an expert in the region who attested that the video footage shot from the Iranian border was genuine.
Azerbaijan barred the European Parliament because it said it would only accept a delegation if it visited Armenian-controlled territory as well. "We think that if a comprehensive approach is taken to the problems that have been raised," said Azerbaijani foreign ministry spokesman Tahir Tagizade, "it will be possible to study Christian monuments on the territory of Azerbaijan, including in the Nakhchivan Autonomous Republic."
After several more postponed visits, a renewed attempt was planned by PACE inspectors for August 29 - September 6 2007, led by British MP Edward O'Hara. As well as Nakhchivan, the delegation would visit Baku, Yerevan, Tbilisi, and Nagorno Karabakh . The inspectors planned to visit Nagorno Karabakh via Armenia, and had arranged transport to facilitate this. However, on August 28, the head of the Azerbaijani delegation to PACE released a demand that the inspectors must enter Nagorno Karabakh via Azerbaijan. On August 29, PACE Secretary General Mateo Sorinas announced that the visit had to be canceled because of the difficulty in accessing Nagorno Karabagh using the route required by Azerbaijan. The Ministry of Foreign Affairs in Armenia issued a statement saying that Azerbaijan had stopped the visit "due solely to their intent to veil the demolition of Armenian monuments in Nakhijevan.