"Despite this, we all hoped for an early resolution to the problems and the removal of the armed structures from the region to avoid further complication of the situation," the letter said.
But Wednesday's killing of Imumnazarov -- who had called for a peaceful resolution to the conflict -- "could provoke a further escalation of the situation and result in heavy casualties," it said. "And this, in turn, could become a pretext for the destruction of peace and accord in Tajikistan, as well as in the whole Central Asian region."
The letter asked that Rahmon and other government representatives "intervene in this complex situation as we believe that a purposeful process of destabilization is taking place in the country by third forces."
It did not elaborate on who those third forces might be.
Imumnazarov's killing was preceded in July, before the peace agreement was reached, by the killing of Sabzali Mamadrizoev, a representative of the opposition Islamic Renaissance Party. He had condemned what he said was the government's indiscriminate attack on residents of Khorog after a general was killed there.
A YouTube video shows soldiers dragging a man through the city streets and dumping him in a trash heap. Residents identified the man as Mamadrizoev; the government said it wasn't he. The residents have said they want the soldiers involved in the killing to be brought to justice.
Islamic Renaissance Party national leader Muhiddin Kabiri said in a statement that even if even if the dead man was not Mamadrizoev, he should have been treated humanely.
Tajikistan gained independence with the collapse of the Soviet Union in 1991 but was troubled by a five-year civil war that ended in 1997 and is still plagued by widespread corruption and poverty.
Tensions remain high between the Tajik government in the capital city of Dushanbe and warlords -- so-called Komandos -- of Gorno-Badakshan, who are members of the Pamiri ethnic minority.
The region was a stronghold of rebels during the civil war, which claimed thousands of lives. The war divided people along ethnic and regional lines, and the Pamiri largely sided with the opposition.
A United Nations-brokered peace plan left Rahmon's secular government in place but gave official jobs to some of his opponents, including the Komandos.
Rahmon, who has Moscow's support and faces reelection next year, has sought to consolidate power and stamp out remnants of the former opposition-turned-warlords.