Aitmatov, whose mythical novels and stories were widely acclaimed in the former Soviet Union and translated into more than 170 languages, died at a clinic in the southern German city of Nuremberg on June 10.
"Today we are faced with the greatest of losses: Merciless death has taken Chingiz Torokulovich Aitmatov from us," President Kurmanbek Bakiev told local and foreign dignitaries in a eulogy at the National Philharmonic before the ceremony in Bishkek's central Alatoo Square.
"One more star in the sky has faded; the heart that was filled with joy and sorrow, pure feelings and dreams of not only the Kyrgyz nation but also of all the peoples of the world, has been stilled, has stopped."
Following the tribute ceremony in downtown Bishkek, the coffin of the man who was regarded by many as the conscience of a nation was taken to the Fathers Graveyard (Ata-Beyit) Memorial Complex on the outskirts of the city for burial.
The memorial complex was erected in 1992 to inter the victims of Stalinism, including Aitmatov's father, Torokul Aitmatov. The name "Ata-Beyit" was given by Aitmatov, who in the 1980s was one of the first Kyrgyz writers to openly expose the Stalinist purges.
UNESCO has described Aitmatov as one of the world's most-read contemporary authors. Aitmatov coined the term "mankurt" in his novel "The Day Lasts More Than 100 Years," about a Kazakh man who is torn between tradition and Soviet manipulation traveling to bury a dear friend.
A number of Aitmatov's books have been adapted into films in Kyrgyzstan, Russia, and Turkey.
He had suffered lung and kidney failure after falling ill three weeks ago while on a film set.
Kazakh poet and former Ambassador to Bishkek Mukhtar Shahanov eulogized Aitmatov in verse at the National Philharmonic ceremony, saying Aitmatov had conquered the world with his writings.
"Two people named 'Chingiz' were famous in world history," Shahanov said. "One [Mongol conqueror Chingiz Khan] conquered the world with his sword, while the other conquered the world with his spiritual power."
The writings of Aitmatov, son of a Kyrgyz father and Tatar mother, transcended ethnic barriers such that many Central Asians -- and indeed citizens all over the former Soviet Union -- considered him to be "their" writer.
His insightful but tempered portrayals of life in the Soviet Union earned him widespread public respect while they allowed him to avoid bans or outright criticism from Soviet authorities.
In Bishkek for the memorial ceremonies, Russian Culture Minister Aleksandr Avdeyev praised Aitmatov, who wrote in both Kyrgyz and Russian.
"Today we are burying a giant of world literature of the 20th century," Avdeyev said, "a giant of Kyrgyz literature, a giant of Russian literature."
After the disintegration of the Soviet Union in 1991, Aitmatov served as a diplomat for a newly independent Kyrgyzstan and a member of the Kyrgyz parliament. In 1997, he became the first person to be granted the official title "Hero of Kyrgyzstan."
Aitmatov leaves behind a wife, three sons, and a daughter.