Washington (CNN) President Donald Trump spent the weekend firing off tweets that took aim at the Department of Justice and the FBI in the wake of the guilty plea by his former national security adviser, Michael Flynn.

Trump has frequently criticized the agencies over their handling of the Russia investigation, and his comments over the weekend were met with fierce pushback from former Justice Department officials.

"I had to fire General Flynn because he lied to the Vice President and the FBI," Trump tweeted Saturday morning. "He has pled guilty to those lies. It is a shame because his actions during the transition were lawful. There was nothing to hide!"

The tweet raised questions as to whether Trump knew Flynn had lied to the FBI when he fired him in February. On Sunday, Trump's personal lawyer, John Dowd, said he was the person who drafted it.

Flynn pleaded guilty Friday to lying to the FBI about conversations with Russia's ambassador during the transition and disclosed that he is cooperating with the special counsel's office in its Russia investigation.

The President also zeroed-in on the FBI and the Justice Department for not being harsher in its investigation of presidential candidate Hillary Clinton's handling of emails while secretary of state.

"So General Flynn lies to the FBI and his life is destroyed, while Crooked Hillary Clinton, on that now famous FBI holiday 'interrogation' with no swearing in and no recording, lies many times...and nothing happens to her?" Trump tweeted . "Rigged system, or just a double standard?"

He also alluded to Clinton's use of Bleachbit to delete personal emails.

"Many people in our Country are asking what the 'Justice' Department is going to do about the fact that totally Crooked Hillary, AFTER receiving a subpoena from the United States Congress, deleted and 'acid washed' 33,000 Emails? No justice!" Trump posted Saturday evening.

And on Sunday, Trump continued his focus on Flynn and fired FBI Director James Comey, referencing Comey's testimony to the Senate Intelligence Committee in June that Trump pressed him to end the investigation into Flynn.

"I never asked Comey to stop investigating Flynn," Trump said . "Just more Fake News covering another Comey lie!"

"After years of Comey, with the phony and dishonest Clinton investigation (and more), running the FBI, its reputation is in Tatters - worst in History! But fear not, we will bring it back to greatness," he later added

Sunday's tweets about the FBI being in "tatters" came alongside the news that a senior FBI official was removed last summer from special counsel Robert Mueller's investigation into Russian meddling in the 2016 election after an internal investigation found the official sent messages that could be interpreted as showing political bias for Clinton and against Trump.

Reaction to tweetstorm

The FBI has so far not responded to Trump's tweets about the bureau, but they garnered criticism on social media and elsewhere. Comey posted a defense of the FBI on Instagram Sunday night, quoting his own testimony before the Senate Intelligence Committee in June.

‪"'I want the American people to know this truth: The FBI is honest. The FBI is strong. And the FBI is, and always will be, independent.' ‪Me (June 8, 2017),"‬ Comey wrote.

Former acting Attorney General Sally Yates tweeted a response as well: "The FBI is in 'tatters'? No. The only thing in tatters is the President's respect for the rule of law. The dedicated men and women of the FBI deserve better."

The FBI is in "tatters"? No. The only thing in tatters is the President's respect for the rule of law. The dedicated men and women of the FBI deserve better. — Sally Yates (@SallyQYates) December 4, 2017

"The FBI's reputation is not in 'tatters'. It's composed of the same dedicated men and women who have always worked there and who do a great, apolitical job," he tweeted. "You'll find integrity and honesty at FBI headquarters and not at 1600 Penn Ave right now(.)"

And fellow Republican Sen. Lindsey Graham, of South Carolina, said to tread lightly.

"There's an ongoing criminal investigation. Comey may be part of it," Graham told CBS's "Face the Nation." "You tweet and comment regarding ongoing criminal investigations at your own peril. I'd be careful if I were you, Mr. President."

The FBI Agents Association also defended the bureau Sunday night, putting out a statement from the group's president, Thomas O'Connor, on Twitter.

"Every day, FBI Special Agents put their lives on the line to protect the American public from national security and criminal threats," the statement read. "Agents perform these duties with unwavering integrity and professionalism and a focus on complying with the law and the Constitution.