Manafort's lawyers did not immediately return messages from The Associated Press.
Assange's Ecuadorian lawyer, Carlos Poveda, said the Guardian report was false.
The Guardian report, which was based on unnamed sources, claimed that Manafort had met Assange in the Ecuadorean embassy in London, in 2013, 2015 and 2016. He had been in the room for the Trump Tower meeting with Russians who touted they had incriminating information about Hillary Clinton; and he had allegedly offered private briefings on the campaign to a Russian oligarch to whom he was indebted, according to The Washington Post.
There was no detail on what might have been discussed. He was promoted to campaign chairman in May 2016.
A prosecutor apparently used the Assange mystery matter as a legal template to write a motion to seal the case of a man accused in an unrelated sex crimes investigation. But it was not clear what charges Assange would face.
The official WikiLeaks Twitter account also refuted the claim, saying that: "This is going to be one of the most infamous news disasters since Stern published the 'Hitler Diaries'".
Julian Assange on the balcony of the Ecuadorian Embassy in London in 2017.
Ecuadorian Intelligence Claims Paul Manafort Met With Julian Assange Prior to DNC Hack
But prosecutor Gordon Kromberg said no precedent exists for a judge to require disclosure of criminal charges before a defendant's arrest.
A decision whether to unseal USA government charges against Julian Assange was delayed for a week by Judge Leonie Brinkema in the United States District Court for the Eastern District of Virginia on Tuesday.
Also, the report states a "separate internal document written by Ecuador's Senain intelligence agency and seen by the Guardian lists "Paul Manaford [sic]' as one of several well-known guests".
It says the government considered alternatives to sealing, but that any procedure "short of sealing will not adequately protect the needs of law enforcement at this time because, due to the sophistication of the defendant and the publicity surrounding the case, no other procedure is likely to keep confidential the fact that Assange has been charged".
US District Judge Leonie Brinkema pressed Townsend for any precedent requiring criminal charges to be unsealed prior to arrest.
Among the changes they noted was the "hermit-like" appearance of Assange and the absence of the cat, which had been his only permanent companion within the embassy walls.
The report comes as Manafort faces an accusation of lying to Special Prosecutor Robert Mueller, who's investigating Russian interference in the 2016 U.S. presidential election.