Comey reportedly asked the US Justice Department (DOJ) to publicly reject Trump's allegation as he believed there was no evidence to support Trump's "highly-charged claim", according to The New York Times and NBC.
He is said to have asked for this because the allegation falsely insinuated that the FBI broke the law.
Neither did the White House nor did the FBI and the Department of Justice respond immediately to the reports on Comey's unusual comments, which were based on unnamed sources.
According to the daily, Comey, who made the request on Saturday after Trump levelled his allegation on Twitter, has been working to get the Justice Department to knock down the claim because it falsely insinuates that the FBI broke the law.
The New York Times described the FBI request as remarkable.
Trump had accused Obama of "wire tapping" his office in New York just before the 2016 presidential elections and likened the alleged surveillance of his communications to the "Watergate" scandal.
"How low has President Obama gone to tapp my phones during the very sacred election process. This is Nixon/Watergate. Bad (or sick) guy!" he said.
Obama's spokesperson Kevin Lewis rejected the allegations as "simply false" and said the former US president never ordered surveillance on any US citizen.
Multiple former senior US officials have dismissed Trump's allegations against Obama, however, calling them "nonsense" and "false."
Former Director of National Intelligence James Clapper said that Trump was not wiretapped by intelligence agencies nor did the FBI obtain a court order through the Foreign Intelligence Surveillance Act to monitor Trump's phones.
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