SOCHI, Russia—Differences over the war in Libya and missile defense are hindering efforts to build a strategic partnership between NATO and Russia, Russia’s foreign minister said Monday.

“The dialogue is not proceeding as easily as we expected after the Lisbon summit,” Sergey Lavrov said. He was referring to the meeting of Russia’s and NATO’s heads of state in the Portuguese capital in November, when the former Cold War rivals decided to forge a close partnership.

NATO Secretary-General Anders Fogh Rasmussen acknowledged the differences but insisted that “the spirit of Lisbon lives on and continues to guide us. Cooperation is the best choice, partnership is the only path forward.”

Envoys from the alliance’s 28 members and Russia were in the resort city of Sochi for a meeting of the NATO-Russia Council, which normally meets at NATO’s headquarters in Brussels.

Russia has repeatedly criticized the alliance’s bombing of Libya, saying it violates a U.N. resolution calling for a no-fly zone and the protection of Libyan citizens.

“Since NATO started to execute the U.N. resolution … we have discussed how strongly international law has been respected,” Lavrov told journalists.

Rasmussen stated that was the case. “Everything NATO does … is in full compliance with the UN mandate.”

Asked whether Moamar Gadhafi should stay in office, Rasmussen said “it is for the Libyan people to shape the future of their country. The mission we are conducting aims at meeting very specific military objectives.”

“I would stress that the only acceptable solution is to accommodate the legit aspirations of the Libyan people and see a transition to a fully fledged democracy.”

Lavrov also said differences remain over a proposed missile-defense system in Europe, which Rasmussen acknowledged.

“Many key issues need to be addressed. We never said we would agree on ballistic missile defense in a few weeks or months,” Rasmussen said. “But we are determined to keep up the dialogue and keep up the work, and we are making progress.”

Russia is demanding to jointly run the system, while the United States and NATO are offering Moscow a more limited role. Experts from both sides are scheduled to report this month on details of the proposal, but the two sides still haven’t come up with a good understanding of how a joint program would work.

Rasmussen said the military alliance and Russia must build on their cooperation in the Afghan war and the fight against maritime piracy to create a solid strategic partnership.

He said the two sides “are not yet there but are making progress.”

Relations between NATO and Russia have roller-coastered over the past decade, reaching a high point after the September 2001 terrorist attacks. But the ties hit rock-bottom following the 2008 Russio-Georgian war, when the alliance—under pressure from the Bush administration—froze relations with Moscow.

Under the Obama administration’s resetting of ties with Russia, Moscow has agreed to allow NATO to ship military supplies to Afghanistan through its territory, and has cooperated in anti-piracy patrols off the Somali coast. Russian forces have also trained with NATO in anti-terrorism and naval exercises.

In addition, Russia has supported U.N. sanctions against Iran and signed the New START treaty reducing the ceiling on both countries’ nuclear arsenals.