Judge Sullivan did not set a new date for sentencing but asked Mr Mueller's team and Mr Flynn's attorney to give him a status report by March 13.
The judge added: "I can't hide my disgust, my disdain". It also provides a glimpse of how hard things can get when prosecutors from Mueller's team and NY begin turning the screws at the same time.
Prosecutors hadn't recommended prison, citing Flynn's extensive cooperation with investigators looking into Russian election interference.
Russian Federation collusion investigation head Robert Mueller had proposed Flynn receive no jail time for lying to investigators about his Moscow ties. The hearing upset what had been a carefully crafted agreement and pushed months into the future a resolution of one of Mueller's signature prosecutions.
He later softened his tone, apologizing for suggesting that Flynn had worked as a foreign agent while in the White House when that other work had actually already ended.
"The FBI broke standard protocol in the way they came in and ambushed General Flynn and in the way they questioned him", she said. But these statements reflect a kind of abiding bias that might well result in reversible error if Flynn's lawyers appeal a sentence he eventually receives from Sullivan.
Still, a judge who addressed the former adviser in court on Tuesday emphasized the gravity of his actions.
The hearing took place amid escalating legal peril for the president, who was implicated by federal prosecutors in NY this month in hush-money payments to cover up extramarital affairs. Almost a half-dozen former aides and advisers have pleaded guilty, agreeing to co-operate with prosecutors. Some, like Flynn, were tripped up by concealing Russian contacts.
The White House continues to stand in support of Flynn, "wishing him well" and attacking the Federal Bureau of Investigation of questioning him wrongly and not allowing him to have a White House legal counsel with him while he sat down with the investigating team.
Andrew Napolitano questioned Trump's judgment after it was revealed Flynn had lied to the Federal Bureau of Investigation.
The US intelligence services listened in on the phone calls and later put pressure on Flynn over his lies.
White House spokeswoman Sarah Sanders said following Tuesday's hearing that Flynn had been mistreated.
"Arguably, you sold your country out".
But while Sullivan tested those arguments, he was ultimately unmoved and Flynn mostly walked them back. Neither he nor his lawyers disputed that he'd lied to agents.
At one point, Judge Sullivan asked the prosecutor whether the special counsel's office had ever considered charging Flynn with treason.
Sullivan gave Flynn an opportunity to challenge the circumstances and Flynn said "No".
The request came after Judge Sullivan warned Flynn that if he were sentenced as scheduled on Tuesday, he might not get all the credit for his co-operation with investigators that he is entitled to.
Sullivan deliberately telegraphed his intention to impose a prison sentence in defiance of the joint recommendation of the Mueller and Flynn's defense attorney, who agreed that Flynn should not serve any prison time. Reading the McCabe memo filed by the Special Counsel with the court last Friday, however, we see that Flynn believed that his conversations were probably intercepted and known to the Federal Bureau of Investigation.