Navalny, 47 when he died, was Putin's fiercest domestic critic.
His allies, branded extremists by the authorities, accused Putin of having him murdered and have said they will provide proof to back their allegation.
The Kremlin has denied any state involvement.
In March, Putin called Navalny's demise "sad" and said he had been ready to hand the jailed politician over to the West in a prisoner exchange provided Navalny never returned to Russia.
Navalny's allies said such talks had been under way.
Vladimir Putin has said he had been ready to hand Alexei Navalny to the West in a prisoner exchange. (AP PHOTO)
The Journal, citing unnamed people familiar with the matter, said on Saturday that US intelligence agencies had concluded that Putin probably did not order Navalny to be killed in February.
It said Washington had not absolved the Russian leader of overall responsibility for Navalny's death however, given the opposition politician had been targeted by Russian authorities for years, jailed on charges the West said were politically motivated, and had been poisoned in 2020 with a nerve agent.
The Kremlin denies state involvement in the 2020 poisoning.
Kremlin spokesman Dmitry Peskov said on Saturday he had seen the Journal's report, which he said contained "empty speculation".
"I've seen the material," Peskov told reporters when asked about the matter.
"I wouldn't say it's high-quality material that deserves attention."
Reuters could not independently verify the Journal report, which cited sources as saying the finding had been "broadly accepted within the intelligence community and shared by several agencies, including the Central Intelligence Agency, the Office of the Director of National Intelligence, and the State Department's intelligence unit".
The US assessment was based on a range of information, including some classified intelligence, and an analysis of public facts, including the timing of Navalny's death and how it overshadowed Putin's re-election in March, the paper cited some of its sources as saying.
It cited Leonid Volkov, a senior Navalny aide, as calling the US findings naive and ridiculous.
