The North's plan to launch a long-range rocket next month has overshadowed the 53-nation summit, which is meant to focus on the threat of uranium and other nuclear material from falling into the hands of terrorists.
Obama has devoted much of his three-day South Korean visit to its wayward neighbour, repeatedly denouncing the rocket launch while emphasising the United States is not hostile to the North's people.
North Korea responded on Tuesday by saying it would go ahead with what it calls a peaceful satellite launch, saying every nation has this right, and called on Obama to drop his "confrontational mindset".
"The US head of state said he had no hostile intention towards us," said a Pyongyang foreign ministry spokesman quoted by the official KCNA news agency.
"But if that remark is genuine, he should abandon the confrontational mindset that tries to block us, and should have the courage to admit that we have as much right to launch our satellite as other countries do."
The North said it would judge whether Obama's remarks were genuine "or just another hypocrisy" depending on whether his country applies a double standard to the launch.
The United States, Japan, South Korea and other countries say the launch would in fact be a long-range missile test, banned under UN resolutions and breaching US-North Korean deal last month.
Obama on Monday made an unusual, direct appeal to the North's new leaders to "have the courage to pursue peace". There would be no more rewards for provocations, he said in reference to its launch.
Chinese President Hu Jintao, whose country is North Korea's sole major ally, also reportedly expressed serious concern at Pyongyang's plan during a meeting on Monday with Obama.
On Tuesday's second and final day of the summit, Obama was focused on the nuclear threat from "non-state actors" and not the nuclear-armed North.
"The security of the world depends on the actions that we take," he said in a speech to delegates at the start of the day.