Baku had no choice but to take matters into its own hands, the president added.
"I warn those who support this rogue state in its occupation of Upper Karabakh will answer to the common conscience," Erdoğan said as referring to Armenia.
In his opening speech, parliament speaker Mustafa Şentop said that Turkey will continue to support Azerbaijan in their rightful cause.
He recalled relations between Turkey and Azerbaijan are exemplary.
"The principle of 'two states, one nation,' is not only a slogan or a historical resolve, but also a principle that dominates Turkey-Azerbaijan relations," he noted.
Border clashes broke out last Sunday when Armenian forces targeted Azerbaijani civilian settlements and military positions, leading to casualties.
Azerbaijan's parliament declared a state of war in some of its cities and regions following Armenia's border violations and attacks in the occupied Upper Karabakh, also known as Nagorno-Karabakh, region.
On Monday, Azerbaijan declared partial military mobilization amid the clashes.
