Armenia's president on Tuesday refused to sign off on an order to dismiss the head of the military, exacerbating a political crisis sparked by last year's war with Azerbaijan.

Prime Minister Nikol Pashinyan last week accused the army's chief of staff of staging a coup after he called for Pashinyan to resign.

The prime minister has come under increasing pressure to step down for his handling of last year's war over the disputed Nagorno-Karabakh region, which saw Armenia suffer heavy losses and agree to hand over swathes of territory to Azerbaijan.

President Armen Sarkisian's office said Tuesday that he "did not sign the prime minister's decree to dismiss" chief of general staff Onik Gasparyan.

However Pashinyan's decree will automatically enter into force in three days' time, according to the constitution.

Gasparyan's call for Pashinyan to resign last week sparked large protests, with the prime minister's supporters and critics flooding the streets of the capital Yerevan.

The row with top generals began when Pashinyan fired the deputy chief of the general staff.

His dismissal came after he ridiculed claims by the prime minister that Iskander missiles supplied by Russia — Armenia’s main military ally — had failed to hit targets during the war for Nagorno-Karabakh.

Pashinyan issued a subdued retraction on Monday, with his office saying he had been "incorrectly briefed on this matter” and had no doubts about the quality of Russian military production.