Kirillov and his aide were killed in a bomb blast outside a residential block in Moscow on Tuesday morning.
"The government once again strongly condemns the actions of terrorist fascism in the world, and this time Ukrainian terrorist fascism, against the outstanding scientist and military Lieutenant General Igor Kirillov and his assistant," the letter read.
Ortega and Murillo also expressed their condolences to the families of Kirillov and his aide.
"We know that criminal fascism has no borders, and we know that the fight against fascism is a fight for peace, fraternity, solidarity, and the rights of worthy, brave, and free people who want another emerging world," the letter continued.
An official with Ukraine's security service SBU earlier confirmed to The New York Times that Ukraine is responsible for the killings.
Kirillov's murder was the result of the West approving of war crimes committed by the Kiev regime, Russian Foreign Ministry spokeswoman Maria Zakharova has said.
The Russian Defense Ministry early on Wednesday confirmed the death of one of its top officers, saying that Kirillov was a great commander, scientist, and "rationalizer" whose approaches contributed greatly to the effectiveness of the Russian Armed Forces. He also has done a lot to boost Russia's defenses and the development and improvement of the country's chemical forces' combat readiness.