Turkish leaders are seeking to put relations with Azerbaijan back on track after tensions between the two allies peaked with a diplomatic note of protest handed over to Azerbaijani officials due to their decision to remove a Turkish flag from in front of an embassy building in Baku. President Abdullah Gül spoke to his Azerbaijani counterpart, İlham Aliyev, on the phone to do away with "misunderstandings." In addition, Foreign Minister Ahmet Davutoğlu is to meet with both Aliyev and the Azerbaijani foreign minister today to assure Baku that Turkey monitors and protects Azerbaijan's national interest in its process of rapprochement with Armenia.

Turkey's ambassador to Azerbaijan, Hulusi Kılıç, delivered the note of protest to officials at the Azerbaijani Foreign Ministry after it was heard in Ankara that the flag in front of the Religious Affairs Consultancy Office, affiliated to the Turkish Embassy, was removed this morning. The note underlined that the building had diplomatic status according to the 1961 Vienna Convention on Diplomatic Relations, thus Turkey had the right to have its flag in front of the building.

The dispute emerged as the government sent two protocols signed with Armenia on normalizing relations to Parliament. Azerbaijan, which fought a war with Armenia over Nagorno-Karabakh in the early 1990s, says the restoration of Turkish-Armenia ties will harm its national interests. Turkey severed its ties and closed the border with Armenia in 1993 in a show of solidarity with Azerbaijan.

Tensions escalated when Turkish authorities, upon the demand of world soccer's governing body FIFA, banned Azerbaijani flags in a World Cup qualifying game between the Turkish and Armenian national teams earlier this month. The Azerbaijani decision to remove Turkish flags in front of a monument in the memory of fallen Turkish soldiers and the building of the Religious Affairs Consultancy Office has apparently come in response to the ban on Azerbaijani flags during the soccer game.

Despite delivery of the note, diplomatic sources in Ankara, speaking with Today's Zaman, underlined that “channels of dialogue” are open with Baku and that the note should not be considered a sign of crisis since it was a procedural implementation in customary practice regarding diplomacy.

As a result of the phone call between President Gül and his Azerbaijani counterpart, Aliyev, “misunderstandings and misperceptions which stemmed from some emotional reactions that have emerged while passing through a difficult process, have been overcome,” sources at Gül's office said. They noted that Gül also briefed Aliyev about his recent telephone conversations with both US President Barack Obama and Russian President Dmitry Medvedev, in which he urged both leaders to step up efforts to resolve the Nagorno-Karabakh dispute.

Foreign Minister Davutoğlu, meanwhile, will today have talks with both Aliyev and his Azerbaijani counterpart, Elmar Mammadyarov, during a visit to Baku which will take place on the occasion of a foreign ministerial meeting of the Organization of the Black Sea Economic Cooperation (BSEC) hosted by Azerbaijan.

“Mr. Davutoğlu will have talks in Baku concerning recent developments in normalization of Turkish-Armenian relations as well as in relations between Azerbaijan and Armenia,” diplomatic sources, speaking on the condition of anonymity, told Today's Zaman on Wednesday.

As of Monday, Davutoğlu, in strongly worded remarks, once more made clear that there is no place for speculation regarding Turkey's policy concerning an end to the occupation of Nagorno-Karabakh as a fundamental national cause. His remarks came when he was reminded of the fact that Turkish flags around the monument to 1,130 Turkish soldiers who died while fighting for Azerbaijan's independence in 1918 were taken down by the mayor of Baku's Sabayil district on Thursday.

While addressing members of the Turkish Parliament during a session on two protocols signed between Armenia and Turkey for re-establishing ties and reopening their joint border, Davutoğlu reiterated on Wednesday that Turkey's firm support for the protection of Azerbaijan's territorial integrity will continue.

Two separate groups from the Parliament, the first composed of deputies of the ruling Justice and Development Party (AK Party) and the Nationalist Movement Party (MHP) and the second composed of deputies of the main opposition Republican People's Party (CHP), are planning to visit Baku on Sunday in order to ease Azerbaijan's concerns.

Last week, only a day after the flag move which disappointed Turkey, Aliyev expressed dissatisfaction with Turkey's terms for natural gas trade, suggesting that his energy-rich Caspian Sea country could seek other avenues for exports. Aliyev's remarks suggested that Azerbaijan's dismay over Turkey's efforts to reconcile with foe Armenia could hurt Western hopes of reducing the European Union's reliance on Russia for gas.

On Tuesday, Prime Minister Recep Tayyip Erdoğan stated that those who want to exploit the ban by FIFA during the Turkey-Armenia game were doing nothing but “provocation.”

“We never take a step that could disturb our Azerbaijani brothers. Let them be sure about this. For us, the Azerbaijani flag is as sacred as Azerbaijani soil. Our martyrs resting in Baku are witnesses of this understanding. Let no one test Turkey's sincerity. We should be on alert against provocations. Our Azerbaijani brothers will soon understand what the removal of the Turkish flag in Baku means,” Erdoğan said.