Mr Mueller’s team was responding to a sentencing memo from Flynn’s lawyers criticising the FBI interviews with their client, saying agents did not provide him “with a warning of the penalties” for misleading investigators.
“A sitting National Security Adviser, former head of an intelligence agency, retired Lieutenant General, and 33-year veteran of the armed forces knows he should not lie to federal agents,” Mr Mueller's office said in its court filing.
“He does not need to be warned it is a crime to lie to federal agents to know the importance of telling them the truth.”
Flynn pleaded guilty in December 2017 to lying to the FBI agents about his conversations with Russia's then-ambassador, Sergei Kislyak, and has been cooperating with Mr Mueller's probe into Russia's meddling in the 2016 election and possible collusion between Moscow and Trump campaign officials.
The FBI interview took place on 24 january 2017, soon after Mr Trump took office.
In the filing Mueller said Flynn lied to the media and senior administration officials in the weeks leading up to the interview, telling them he had not discussed US sanctions against Russia with Mr Kislyak when in fact he had.
“Thus, by the time of the FBI interview, the defendant was committed to his false story,” Mr Mueller's prosecutors wrote.
Mueller's filing was in response to an order by the judge to turn over documents related to the interview.
That order, in turn, followed a sentencing memo earlier this week by Flynn's lawyers in which they argued for leniency.
As mitigating factors, Flynn's lawyers cited both the lack of a warning about lying and a suggestion by then-FBI Deputy Director Andrew McCabe to Flynn that the “quickest way” to conduct the interview was without counsel present.
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Hello and welcome to our liveblog bringing you the latest development on Special Counsel Robert Mueller's investigation.
The special counsel's office is pushing back at the suggestion that the FBI acted improperly in its interview of former national security adviser Michael Flynn.
Michael Flynn's lawyers said in a sentencing memorandum this week that Flynn was not warned during his interview with the FBI that it was a crime to lie to federal agents.
But prosecutors with special counsel Robert Mueller say Flynn had lied to the White House about his contacts with the Russian ambassador well before the January 2017 interview and merely repeated the same falsehoods when approached by the FBI.
Mr Flynn is scheduled to be sentenced next week for lying to the FBI.
As part of the investigation into possible collusion between Russia and the Trump campaign over election meddling, Special counsel Robert Mueller’s team has filed a two-part sentencing memo for Michael Flynn with a recommendation for a light sentence that has major implications for the probe.
You can read more about what this sentencing recommendation may mean for President Trump here:
Last week, Mr Mueller's team had put out their sentencing memo on Flynn. Some of it was redacted, but the major suggestion was that Flynn should serve little to no jail time.
In prior sentencing documents, Flynn's lawyers and the special counsel had both recommended a light sentence for the highly decorated US Army veteran.
On Tuesday, Flynn's legal team asked for the judge to sentence the 60-year-old Flynn to one year of minimally supervised probation and 200 hours of community service.
That request came a week after the special counsel recommended that Flynn receive a sentence “at the low end” of his guideline range of zero to six months in jail.
In the latest filing, the key quote from Mr Mueller's team appears to be this one:
The filing comes as Mr Mueller's office releases documents detailing its latest expenses.
From April through to September, the special counsel's office directly accounted for $4.6 million in expenses. Another $3.9 million was spent by other government officers supporting the investigation. That adds to the more than $16.7 million spent through March.
About $2.9 million went toward salaries and benefits. The special counsel also spent about $580,000 on travel.
The Russia investigation has cost more than $25 million since the special counsel's May 2017 appointment, when adding the latest figures.
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