Mayor Tomihisa Taue said Japan's inaction "betrayed expectations of the global community."
Japan refused in April to sign an unconditional pledge by nearly 80 countries to never use nuclear weapons.
The document, prepared by a U.N. committee, is largely symbolic because none of the signatories possesses nuclear weapons. Countries with nuclear arsenals that have not signed it include the United States, Russia, India and Pakistan.
Japan does not have nuclear weapons and has pledged not to produce any, although some hawkish members of the ruling party say the country should consider a nuclear option.
Taue said that as the world's only victim of atomic bombings, Japan's refusal to join the initiative contradicts its non-nuclear pledge.
"I call on the government of Japan to return to the origin of our pledge as an atomic-bombed country," he said at the peace park near the epicenter of the 1945 blast.
Tokyo apparently refused to sign the document because of its security arrangement with the United States, which could allow the U.S. an option to deploy nuclear weapons from Japan to counter the threat of North Korea.
That suggests that Japan's government would approve the use of nuclear weapons under some circumstances, Taue said.
About 6,000 people, including U.S. Ambassador John Roos, attended Friday's ceremony after offering silent prayers for the victims of the U.S. atomic bombings — on Nagasaki on Aug. 9, 1945, and on Hiroshima three days earlier. The bombings prompted Japan's surrender in World War II. The Hiroshima blast killed an estimated 140,000 people, and another 70,000 died in Nagasaki.
Opposition to nuclear power in Japan has risen sharply after a March 2011 earthquake and tsunami ravaged the Fukushima nuclear plant, which spewed radiation and forced the evacuation of tens of thousands of people.
Despite the public's safety concerns, Prime Minister Shinzo Abe is aggressively pushing to export nuclear plants and technology to developing countries, including Turkey and Vietnam, and is trying to step up nuclear cooperation with France and India.
In a speech at the ceremony, Abe did not mention the dilemma Japan is facing over nuclear energy.
He said Japan as the sole victim of nuclear attacks has the duty to achieve a nuclear-free world and keep telling the world of the inhumane side of nuclear weapons.
Copyright 2013 The Associated Press.