The North Atlantic Treaty Organization (NATO) has to respond in different ways to Russia's interference in other political systems, its secretary general told CNBC Saturday.

Authorities in the United States have accused Russia of meddling in the 2016 presidential race. Just on Friday, the Department of Justice indicted 13 Russian nationals and three Russian entities on charges of conspiracy to defraud the U.S. The indictment accused the Russians of seeking to wage "information warfare" and "sow discord" in the American political system.

Speaking to CNBC at the Munich Security Conference, Jens Stoltenberg said that there have been many reports of Russian meddling in NATO countries and that the organization needs to act.

"We've seen many reports and many examples of how Russia is meddling, interfering in democratic political processes in many countries, including in NATO-ally countries and we have to be able to respond to that in many different ways," he said.