Demonstrators marched on the US embassy, where survivors of the US atomic attacks on Hiroshima and Nagasaki delivered a letter urging Mr Obama to do more to cut Washington’s enormous nuclear weapons stockpile.
The president also came under fire for not taking the time to visit the two cities and failing to establish a timetable for a withdrawal from Afghanistan.
At a joint news conference with Japanese Prime Minister Yukio Hatoyama, Mr Obama denied that his administration has been dithering over Afghanistan.
He insisted his next step would not be seen as an “open-ended commitment and that he was bent on “getting this right,” although he did not elaborate further.
Mr Hatoyama – who leads the centre-left Democratic Party which ousted the pro-US administration in August’s elections – said Japan would end a refuelling mission for US occupation forces in Afghanistan.
But he softened the blow by pledging £3 billion for Afghan schools, agriculture and police.
Last weekend over 20,000 people rallied on Okinawa, home to more than half the US forces in Japan, and called on Mr Hatoyama to scrap a 2006 bilateral pact which was signed with former president George W Bush.
Under that agreement around 8,000 US soldiers would remain in Okinawa after 2012 and Japan would foot part of the bill to transfer the rest to Guam.
In September, the government vowed to “re-examine” the 2006 agreement, particularly plans to build a new helicopter base in Okinawa.
But yesterday Mr Hatoyama said: “It will be a very difficult issue, but as time goes by I think it will become more difficult to resolve, so we understand we need to resolve the issue as soon as possible and we will work to do that.”
Japanese Communist Party secretariat head Ichida Tadayoshi called on the Hatoyama government to immediately “initiate diplomatic negotiations with the US government in a forceful manner that completely meets Okinawans’ demands.”
Most islanders were opposed to any realignment of US bases on Okinawa, he stressed.