Mr Stoltenberg did not give an expected date for the two countries to join Nato, but told German news agency DPA he was “absolutely confident” it would happen soon.
Sweden and Finland's applications have for months been held up by the objections of Nato member Turkey.
Although they promised in June to meet Turkish demands on counter-terrorism and weapons exports, Ankara says it has yet to see those pledges fulfilled.
Turkish Foreign Minister Mevlut Cavusoglu said last week that the blocked extradition of a man wanted by Turkey had worsened the atmosphere in talks with Sweden.
“There is a document, it needs to be implemented. We’re not even at the halfway point yet. We're at the beginning,” he said.
Sweden and Finland cannot join Nato until all 30 current allies ratify their application.
Hungary is the only other country yet to do so, but says it has no objection.
Asked whether it would be better if Nato could make a majority decision, Mr Stoltenberg said there was no reason to speculate about a treaty change.
He said allies had other differences of opinion on democracy and the rule of law but that Nato was a useful forum to discuss concerns.
Sweden and Finland already regularly attend Nato meetings and take part in joint exercises.
Both have said they want to join the alliance simultaneously, after Turkey hinted it could say yes to Finland before Sweden.