FBI experts visited Qatar in late May to analyse an alleged cyber breach that saw the hackers place the fake story with Qatar's state news agency, the US broadcaster said.
Saudi Arabia then cited the false item as part of its reason for instituting a diplomatic and economic blockade against Qatar, the report said.
Qatar's government said the May 23 news report attributed false remarks to the emirate's ruler that appeared friendly to Iran and Israel, and questioned whether US President Donald Trump would last in office, according to CNN.
Qatari Foreign Minister Sheikh Mohammed Bin Abdulrahman al-Thani told the broadcaster that the FBI has confirmed the hack and the planting of fake news.
"Whatever has been thrown as an accusation is all based on misinformation and we think that the entire crisis is being based on misinformation," he told CNN.
"It was started based on fabricated news, being wedged and being inserted in our national news agency, which was hacked and proved by the FBI," he added.
World leaders trying to de-escalate Qatar tension
If accurate, the allegations would indicate Russian efforts to undermine US foreign policy, building on US intelligence concerns that Russian hackers attempted to influence last year's presidential election, won by Trump. The Kremlin denies meddling.
Saudi Arabia, Egypt, the United Arab Emirates and Bahrain announced Monday they were severing diplomatic relations and closing air, sea and land links with Qatar.
They accused the tiny Gulf state of harboring extremist groups and suggested Qatari support for the agenda of Saudi Arabia's regional archrival Iran. Qatar has strenuously denied the allegations.
Although Qatar hosts the largest American military airbase in the Middle East, Trump threw his weight behind the Saudi-led effort to isolate the emirate in a surprise move on Tuesday.
US will try to 'resolve' Qatar crisis
He suggested Qatar was funding extremism.
"So good to see the Saudi Arabia visit with the King and 50 countries already paying off," he tweeted in reference to his trip to Riyadh last month.
"They said they would take a hard line on funding... extremism, and all reference was pointing to Qatar. Perhaps this will be the beginning of the end to the horror of terrorism!"
The CNN report quoted the Qatari government communications office as saying it was working with the FBI and Britain's National Crime Agency on an ongoing hacking investigation.
