"Nobody presents firm evidence while talking about the suspected North Korea-Syria links," Song told reporters.
"If Syria received nuclear materials from North Korea, it must have a facility to store them. As far as I know, Syria has no nuclear (storage) facility."
The minister also pointed to discrepancies in the reports on the level of cooperation between Pyongyang and Damascus.
The New York Times and Washington Post reported, citing unnamed sources, that North Korea could be helping US arch-rival Syria build a nuclear weapons facility.
The Washington Post quoted unnamed intelligence sources as saying the Israeli secret service had relayed the information to the US government, which it described as "dramatic."
Kim Myong-Gil, North Korea's deputy UN mission chief, has dismissed the media reports, telling South Korea's Yonhap news agency on Sunday: "They often say things that are groundless."
The United States has long accused North Korea, which carried out a nuclear weapons test in October 2006, of weapons proliferation. US officials have charged Syria with bankrolling terrorism groups in the Middle East.
US Defense Secretary Robert Gates has said that Washington would have a "real problem" if Syria and North Korea were collaborating on a nuclear programme.
"If such an activity were taking place, it would be a matter of great concern because the president has put down a very strong marker with the North Koreans about further proliferation efforts and obviously any effort by the Syrians to pursue weapons of mass destruction would be a concern," Gates said.
"I think it would be a real problem."