"I did no such thing ... never would, I abhor violence," he told parliament on Thursday morning.
Mr Christensen described comparisons of Hitler, Mao, Pol Pot and Stalin to state premiers as "regrettable".
On Wednesday night, he posted a video of his initial speech to his Telegram channel.
"Yes, I called for civil disobedience in the parliament today," he wrote to his 25.5k subscribers.
"Civil disobedience is not violence on the streets - it's 'the refusal to comply with certain laws considered unjust, as a peaceful form of protest'."
Prior to Mr Christensen's speech on Thursday, Labor leader Anthony Albanese demanded Prime Minister Scott Morrison “unequivocally and without reservation” condemn comments made by the Nationals MP that called for a public uprising.
Asked by Mr Albanese in parliament on Wednesday if he would condemn Mr Christensen’s comments, Mr Morrison said he had been “very clear” in denunciating violence, threats and intimidation.
“As a son of a police officer, I believe that everyone should obey the law,” the PM said.
“I, indeed, would condemn any encouragement whatsoever, by any person in any place, regarding acts of civil disobedience. That is not something I would encourage. That's not something I would participate in.”
Unsatisfied with Mr Morrison’s response, Mr Albanese again requested the prime minister “directly condemn the member for Dawson for the very specific comments that he has made”.
Mr Morrison began to quote Sally McManus, secretary of the Australian Council of Trade Unions, before the speaker intervened, asking the prime minister to directly respond to the question.
“I have responded directly to the member's question in denunciating those statements,” Mr Morrison shot back.
Mr Christensen’s comments on Wednesday followed a handful of Coalition senators crossing the floor on Monday to support a bill put forward by One Nation leader Pauline Hanson to overturn vaccine mandates.
Coalition senators Gerard Rennick, Alex Antic, Matt Canavan, Concetta Fierravanti-Wells and Sam McMahon supported One Nation’s bill, defying the government's vote.
Senator Canavan described the vaccine mandates as "unfair, cruel, unnecessary and unAustralian".
Mr Morrison later said his government opposed the bill but defended Coalition senators who had supported the move.
"The Liberal Party and the National Party, we do not run it as an autocracy," he told reporters.
"We don't take people out of our party if we happen to disagree on an issue they feel strongly."
The prime minister was forced to defend his response to the Victorian anti-lockdown protests earlier this month after he was accused by premier Daniel Andrews of "double speak to extremists".
Mr Morrison said disputes needed to be had respectfully “no matter how frustrated people might be” but also declared it was time for the governments of Australia to allow people to make their own choices, urging Australians to “take their lives back”.
Mr Albanese said the prime minister's comments about people’s frustrations had "eliminated any criticism of this activity".
“When people marched on the Victorian parliament with gallows, threatening people with being hung, he spoke about how he understands people’s frustration," he said.
“I ask people to think about that, and whether that represents the leadership that this country needs.”