Stoltenberg told Britain's Telegraph newspaper that NATO members were consulting about deploying more nuclear weapons, taking them out of storage and placing them on standby in the face of a growing threat from Russia and China.
Kremlin spokesman Dmitry Peskov said Stoltenberg's comments appeared to contradict a communique issued at a weekend conference in Switzerland that said any threat or use of nuclear weapons in the Ukraine context was inadmissible.
The talks, held at the behest of Ukrainian President Volodymyr Zelenskiy, were billed as a "peace summit" although Moscow was not invited.
"This is nothing but another escalation of tension," Peskov said of the NATO secretary general's remarks.
Stoltenberg later said Russia was trying to create confusion and that his comments referred to the modernization of NATO's nuclear deterrent, including the replacement of F-16 jets with F-35s and the modernization of weapons deployed in Europe, which he said has been known for a long time.
"Russia is trying a way to always also create a situation where they can blame NATO, and the reality is that NATO is transparent," Stoltenberg told reporters on a visit to Washington.
Comment: Whilst it's clear the West's diplomats are incompetent, Stoltenberg's comments likely were intended to escalate tensions, and his retraction is a lame attempt at deflecting blame onto Russia. Note the projection at the end; accusing Russia of what he himself is so obviously doing.
NATO had earlier sought to clarify Stoltenberg's remarks, saying there were no significant changes to its nuclear posture.
"NATO is committed to ensuring a safe, secure and effective nuclear deterrent," NATO spokesperson Farah Dakhlallah said.
"For that purpose, we have an ongoing modernisation programme to replace legacy weapons and aircraft," she said.
"Beyond that, there are no significant changes to our nuclear deterrent."
Russia, which sent troops into Ukraine in 2022, says the United States and its European allies are pushing the world to the brink of nuclear confrontation by giving Ukraine billions of dollars worth of weapons, some of which are being used against Russian territory. President Vladimir Putin has said Russia is technically ready for nuclear war, and that Moscow could use nuclear weapons to defend itself in extreme circumstances.
Russia and the United States are by far the world's biggest nuclear powers, holding about 88% of the world's nuclear weapons, according to the Federation of American Scientists.
The U.S. has about 100 non-strategic B61 nuclear weapons deployed in five European countries - Italy, Germany, Turkey, Belgium and the Netherlands, according to the Bulletin of the Atomic Scientists. The U.S. has another 100 such weapons within its borders.
Russia has about 1,558 non-strategic nuclear warheads, though arms control experts say it is very difficult to say just how many there are due to secrecy.
It has been that way fror years.