Ben Nimmo, an analyst for US think tank the Atlantic Council, said pro-Kremlin social media accounts had fuelled suggestions the 2014 vote had not been free and fair, and had amplified demands for a re-vote.
Following the No vote, accredited observer Igor Borisov told Russian news agency RIA Novosti the referendum had failed to meet international norms.
His comments were seized upon by those who believed fraud was to blame for a result in favour of Scotland remaining part of the UK.
A YouTube video which advanced those claims proved to be particularly influential and has now been viewed nearly 900,000 times.
Mr Nimmo said that while the majority of social accounts sharing the video were Scottish, a “significant minority” appeared to be pro-Kremlin trolls.
These accounts were among the most vocal amplifiers of the video, posting it repeatedly and tagging different users, he said.
Mr Nimmo’s analysis for the Atlantic Council’s digital forensic research lab was published on Wednesday morning ahead of a discussion of Russian state interference in elections and referendums by an all-party group at Westminster.
Mr Nimmo said: “We know that some genuine voters in Scotland had genuine concerns about the referendum.
“What this shows is that pro-Kremlin Twitter accounts amplified those concerns, and spread the message that the vote was rigged.
“We also know that the Electoral Commission found more voters than ever before had concerns about vote-rigging, partly because of what they read in the media.
“This is worrying because it shows that pro-Kremlin accounts were actively undermining the credibility of the referendum, just as they attacked and undermined the credibility of US democracy in 2016, and it looks like it may have worked.”
Mr Nimmo said he also had suspicions about a petition on Change.org launched by Rally for a Revote, which attracted more than 100,000 signatures.
A similar petition on the UK parliament website attracted 23,700 signatures.
Mr Nimmo said the larger petition had been heavily promoted by pro-Russian Twitter accounts and at least one network of “bot” (short for robot) accounts.
Last month the US Congress published a list of more than 2,700 Twitter accounts with links to the St Petersburg-based Internet Research Agency, sometimes referred to as the “troll factory”.
Researchers at Edinburgh University have identified more than 400 accounts operating out of the agency which have attempted to influence UK politics.
Mr Nimmo said: “We know that, in the US case, over 2,700 Twitter accounts that posed as Americans were run from the ‘troll factory’ in St Petersburg. We simply don’t know how much presence, if any, the troll factory had in Scotland. What the presence of these pro-Kremlin accounts shows is that we need to ask the question.”