The comments came as a published report said North Korea threatened during recent talks in Beijing to export nuclear arms and to add to its arsenal.
Yoon said "verifiable and irreversible" elimination of North Korea's nuclear weapons programs was a requirement in exchange for substantive measures by Washington and Seoul.
North Korea reiterated its stand that a U.S. security guarantee was a precondition for an agreement, and called for Washington to respond to its "new, bold proposal" to resolve the nuclear standoff.
But Yoon said North Korea must take the first step to resolve the dispute, saying Pyongyang had sparked the crisis by violating its international nuclear obligations and nonproliferation rules.
"Only the verifiable and irreversible scrapping of North Korea's nuclear programs can lead to security guarantees and economic aid for the North," Yoon said at a meeting with South Korean journalists.
"The United States and the international community will not reward North Korea for its bad behaviors," Yoon said. "North Korea's policymakers should understand the changed situations in the wake of the Sept. 11 terrorist attacks."
Yoon also stressed stronger security ties between the United States and South Korea to resolve the dispute.
"Rock-solid ties between South Korea and the United States are fundamental to resolving the crisis and building lasting peace on the Korean peninsula," Yoon said at a press conference set up ahead of next week's visit by President Roh Moo-hyun to the United States.
Roh, who took office in February, is scheduled to leave for Washington on Sunday for his first trip to the United States. During his weeklong stay, Roh will meet with President George W. Bush May 14 for talks focusing on North Korea.
Analysts in Seoul say Roh's U.S. trip could be a crucial step in defusing the six-month nuclear crisis.
Ban Ki-moon, Roh's foreign policy adviser, said he expected successful discussions in Washington, adding the two leaders "are of the same age and have the same pragmatic leadership style." Roh and Bush, both 56, have been candid about their views on the communist regime led by Kim Jong Il.
Asked about follow-up measures to last month's nuclear talks in Beijing, Yoon said South Korea, the United States and Japan will discuss a course of action after Bush's meetings with Roh and Japanese Prime Minister Junichiro Koizumi in late May.
During the three-way talks with the United States in China, North Korea offered a "new bold proposal" to defuse the nuclear crisis.
North Korea has yet to elaborate on the proposal, but South Korean officials said it was a comprehensive deal highlighted by North Korea's scrapping of its nuclear and missile programs in return for Washington's security guarantee.
But the Washington Times reported Wednesday threatened during the Beijing talks to export nuclear arms or add to its arsenal, in addition to saying it will test an atomic bomb.
North Korea's negotiator, Li Gun, made the threat during an "aside" session with Assistant Secretary of State James Kelly, said U.S. officials familiar with the closed-door meeting, according to the report.
"This was clearly a threat," said one official. The Times reported the North Koreans also said at the meeting that they have nearly finished reprocessing the 8,000 spent fuel rods that were supposed to be kept in storage under a 1994 agreement with the United States.
Speaking Sunday on NBC's "Meet the Press," Secretary of State Colin Powell said U.S. intelligence cannot confirm the North Korean assertion about reprocessing the spent fuel rods into plutonium for weapons, but he noted, "That's what they say."
"And what they have gotten in response to these statements is nothing from us except condemnation," Powell said.