Pashinyan pushed out the army's chief of staff Onik Gasparyan last month, accusing him of staging a coup after he called for Pashinyan to resign.
But a court on Tuesday ordered that Gasparyan be temporarily reinstated pending a final ruling in an appeal against his dismissal.
Pashinyan's office rejected the ruling, saying "legal acts can't have a retroactive force" according to Armenia's constitution and that "procedures to appoint new chief of staff are under way."
Pashinyan last week appealed to President Armen Sarkisian to appoint Artak Davtyan as new chief of general staff.
Calls for Pashinyan to stand down began in November when he signed a Russian-brokered ceasefire agreement with Azerbaijan that ended six weeks of fighting for Nagorno-Karabakh.
Under the deal -- which many in Armenia see as a national humiliation -- Yerevan agreed to hand over swathes of territory to Azerbaijan.
Both anti-government protesters and Pashinyan's supporters have regularly taken to the streets ever since, as the premier defied calls for his resignation.
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