Russia-NATO council agreed on predictability and transparency under 2001 Vienna document, Stoltenberg said. He added that NATO favors updating it to address snap exercises format.
NATO has briefed Russia on 'important decisions' taken at last week's warsaw summit, Stoltenberg told journalists.
"In the spirit of transparency, NATO briefed Russia on the important decisions we took in Warsaw last week to enhance our security. Russia briefed on the steps they are taking," Stoltenberg said at a press briefing.
"I would also like to underline that we are looking into how we can make sure that the way we conduct our exercises and our military activities in the most predictable and safe way, meaning that NATO planes routinely fly with transponders on when they fly under NATO command in Europe," Stoltenberg said.
He pointed to different standards and practices among the 28 NATO member states in flying with transponders turned on or off, but maintained the importance of a cohesive approach.
"Regardless of this, it is important to sit down to look into the issue and find out how we can enhance air safety, especially in the Baltic region," Stoltenberg stressed.
He said Moscow raised a proposal on air safety in the Baltic Sea.
"Allies will study this proposal carefully. I welcome that Russia has signaled that it wants to pursue risk reduction measures," Stoltenberg said, adding that he looked forward to further discussions on measures to avoid "incidents, accidents and misunderstandings."
"It was a useful meeting, with frank and open discussions. Ukraine was the first item on our agenda," Stoltenberg said at a briefing, describing the disagreements on the crisis as "profound and persistent."
The Council was "not a meeting of minds," but an opportunity to exchange viewpoints and clarify positions on the crisis, he said, in which NATO and the West accuse Russia of fueling the conflict between the Ukrainian government and pro-independence forces. Moscow insists it is not a party to the hostilities.
"We should all work toward the settlement of the conflict in eastern Ukraine by diplomatic and peaceful means. Doing this would allow Ukraine to develop… and would contribute to an overall improvement in relations between NATO and Russia," Stoltenberg told reporters.