The Armenian Revolutionary Federation (ARF) blamed Behaeddin Shakir for involvement in the Armenian–Azerbaijani War, specifically in the communications between Musavat and the CUP. In the initial stages of this war, the ARF (Armenian Militia) was engaged in armed confrontation with the Azerbaijani forces during which many Muslims were expelled from Baku or went underground. The tide turned when Enver Pasha of the Ottoman Empire begin to move forward with the newly established Army of Islam. Dunsterville ordered the evacuation of the city on September 14, after six weeks of occupation, and withdrew to Iran; most of the Armenian population escaped with the British forces. The Army of Islam and their Azerbaijani allies, led by Nuri Pasha, entered Baku on September 15. However, after the Armistice of Mudros between Great Britain and the Ottoman Empire on October 30, Turkish troops were substituted for those of the Triple Entente. Headed by British general William Thomson, who had declared himself the military governor of Baku, 5,000 Commonwealth soldiers arrived in Baku on November 17, 1918. By General Thomson's order, martial law was implemented in Baku.
Behaeddin Shakir was claimed to be the central figure of the Teşkilat-i Mahsusa. This is sometimes used as proof of a state organized genocide using the tehcir (deportations) process of the Tehcir law. Halil Berktay says that local administrators objected to Behaeddin Shakir's deportation orders and called for his arrest. Dissidents were usually replaced by hardliners; sometimes twice if the replacement was not pliant.
^Düzel, Neşe (2000-10-09). "Ermenileri özel örgüt öldürdü". Radikal (in Turkish). Retrieved 2008-09-03. Osmanlı ordusu ve bürokrasisinin de bunun korkunç bir olay olduğunu algıladığını, bunları valilerden ve garnizon komutanlarından bağımsız olarak fütursuzca yapmış olan özel timlerden iğrendiğini ve hatta Enver ve Talat'ın özel adamı olan Behaeddin Shakir hakkında 1915-16 yıllarında tevkif müzekkeresi çıkaran, onu tutuklamaya çalışan valiler ve garnizon komutanlarının olduğunu görüyoruz.