"The speed and scope of, as well as ways to push for any development in, inter-Korean relations will be decided according to progress in the North Korean nuclear issue," said Unification Minister Kim Ha-Joong.
Seoul would no longer hesitate to raise the nuclear issue in talks with its communist neighbour, Kim said in his first briefing to President Lee Myung-Bak.
Critics accused Lee's two liberal predecessors of making too many concessions to the North in the name of reconciliation.
Kim, quoted by Yonhap news agency, acknowledged the criticism. "Now the ministry is going to change with a new resolution and attitude," he said.
A six-nation nuclear disarmament deal is stalled by a dispute over the North's promised declaration of all its nuclear programmes.
The North, which staged an atomic weapons test in October 2006, says it submitted the list last November. The United States says it has not accounted fully for a suspected uranium enrichment programme and allegations of nuclear proliferation to Syria.
The negotiations group the two Koreas, the US, China, Russia and Japan.
Kim, whose ministry handles inter-Korean relations, said Seoul would not agree on any joint economic programme if it was unlikely to receive public consent and produce a tangible result.
He did not specify whether multi-billion dollar projects agreed at a summit last October would go ahead, but Lee has previously promised to review them.
Lee's predecessor Roh Moo-Hyun has said he did not stress denuclearisation at the summit since the issue was being dealt with at six-party level.
Kim and Lee also pledged to prioritise the return of South Koreans kidnapped by the North, along with reunions of separated families.
Lee said the North would fail to stabilise its regime and ease economic difficulties unless it abandoned its nuclear ambitions.
He reiterated that humanitarian aid to the North, which faces a severe food shortage, would continue regardless of nuclear progress.
But he repeated demands that it resolve the problems associated with South Korean prisoners of war, abductees and separated families.
The president said existing joint projects, such as the Seoul-funded Mount Kumgang resort and the Kaesong industrial park, should continue. But he indicated that longer-term aid to rescue the North's crumbling economy depended on full denuclearisation.
"When such pending (nuclear) issues are settled through international cooperation, we are prepared to cooperate with the North."
Seoul says 485 South Koreans, mostly fishermen, were seized in the Cold War decades following the 1950-1953 Korean conflict and more than 500 prisoners of war were never sent home in 1953.
But it has previously been reluctant to make a major issue of the kidnappings. North Korea denies holding any South Koreans against their will.
Kim also promised to cooperate with the international community and rights groups to improve North Korea's human rights record.
Media reports said South Korea would support a resolution criticising the North's record at the UN Human Rights Council in Geneva this week.