Three former Obama administration officials told NBC News that Mr Obama told his successor not to hire Mr Flynn as national security adviser in an Oval Office meeting last year. The Trump administration fired Mr Flynn three months later, after it was revealed that he mislead Vice President Mike Pence about his conversations with the Russian ambassador.
Mr Flynn served the Obama administration as director of the Defence Intelligence Agency starting in 2012. He resigned from his post in 2014, amid rumours that he had been forced out because of his poor management skills. The Trump campaign hired Mr Flynn as an adviser in 2016.
Mr Flynn was forced to resign for a second time in February, after multiple reports claimed he had discussed US sanctions against Russian with the country's ambassador, Sergey Kislyak. It was later revealed that Mr Flynn took payment from Russian state media outlet RT in 2015, and received $500,000 from the Turkish government last year.
"The president must have complete and unwavering trust for the person in that position," White House Press Secretary Sean Spicer said in February. "The evolving and eroding level of trust as a result of this situation in a series of other questionable instances is what led the president to ask for Gen. Flynn's resignation."
The retired lieutenant general is now under investigation by the inspector general of the Department of Defence for taking payments from a foreign government against Pentagon advisement.
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Mr Spicer said Monday that is is "true" that Mr Obama did not think favourably of Mr Flynn, but attributed this to negative comments Mr Flynn made about the former president during the 2016 campaign.
"If President Obama was truly concerned about General Flynn, why didn’t he suspend General Flynn’s security clearance, which they had just approved months earlier?" Mr Spicer asked.
Two US officials told NBC News, however, that the DIA was not aware of the foreign payments at the time they renewed Mr Flynn's clearance. Mr Flynn has been accused of concealing these payments from the DIA by members of the House Committee on Oversight and Government Reform. The inspector general of the Department of Defence is currently investigating whether Mr Flynn failed to properly alert them of these payments.
Mr Spicer's comments echoed a tweet of Mr Trump's from this morning, in which the president asserted that Mr Flynn was "given the highest security clearance by the Obama Administration."
Mr Spicer said the Obama administration had re-approved Mr Flynn's security clearance in April. The Trump administration did not conduct an additional security review before appointing him national security adviser.
The news of Mr Obama's warning comes as his former attorney general, Sally Yates, is set to testify in front of a Senate subcommittee regarding Russian interference in the US election.
Ms Yates is said to have warned the White House as early as 26 January that Mr Flynn's contacts with Russia exceeded what he had disclosed. The White House has said they reviewed Ms Yates' information, and found nothing wrong with what Mr Flynn had said.
Officials did not specify why Mr Obama warned his successor against hiring Mr Flynn, but said the warnings predated concerns about his contact with the Russian ambassador. One official told NBC that Mr Obama felt Mr Flynn was "not suitable for such a high-level post."Reuse content