Yamaguchi, whose face is permanently disfigured from the 1945 attack on Nagasaki, had been seen as a frontrunner for the award for his work with Nihon Hidankyo, a group of survivors of the nuclear bombings nominated repeatedly for the Nobel.
"I don't understand why Nihon Hidankyo didn't get the award this year. It makes me wonder if the Nobel Peace Prize committee is paying special consideration to a certain country," Yamaguchi, 75, told reporters at his nursing home.
"The United States is responsible for not being able to stop other countries from possessing nuclear weapons," he said.
He said that the Nobel prize winners, the UN nuclear watchdog IAEA and its Egyptian director general Mohamed ElBaradei, must "work harder to stop the possibility of repeating the Hiroshima and Nagasaki tragedies in the future."
In Tokyo, Nihon Hidankyo secretary general Terumi Tanaka, also a nuclear bomb survivor, said the Nobel committee's selection was "very regrettable."
"I feel utmost regret that the prize has gone to a UN agency again," he said, noting the United Nations and Secretary General Kofi Annan won the prize in 2001 when the anti-nuclear group was also a candidate.
"The UN and public organizations are just doing their jobs. I thought the prize would be best suited to an NGO like us who have campaigned against nuclear arms and talked about the bombing experiences over the past 60 years."
Yamaguchi was a 14-year-old schoolboy forced to work at a Mitsubishi arms factory in Nagasaki when a US plane dropped a plutonium bomb on August 9, 1945, killing 70,000 people, most of whom melted or burned to death instantly.
Yamaguchi suffered massive radiation burns over the right side of his chest, back and face, a gruesome sight captured in a widely distributed photograph.
In 1956, he helped found Nihon Hidankyo, which includes survivors of the Hiroshima and Nagasaki attacks.
The group has sent Yamaguchi and other members abroad to lobby to abolish nuclear weapons and share atomic-bomb experiences and has demanded the Japanese government provide compensation for nuclear bomb victims.