Boris Johnson has insisted he "deplores any threats to anybody, particularly female MPs", after he described one MP's safety concerns as "humbug".
The PM also said that "tempers need to come down" in Parliament.
It follows a stormy debate as MPs returned to Parliament after a Supreme Court decision that the suspension of Parliament was unlawful.
Mr Johnson defended his description of a law seeking to block a no-deal Brexit as "the surrender bill".
The law, known as the Benn bill, forces the government to ask for an extension to the Brexit deadline.
During a number of interviews with BBC political editors, the PM argued it would "take away the power of the government... to decide how long it would remain in the EU".
Speaking to the BBC political editor for the North West of England, Nina Warhurst, the prime minister said: "I totally deplore any threats to anybody, particularly female MPs, and a lot of work is being done to stop that and give people the security that they need.
"But I do think in the House of Commons it is important I should be able to talk about the surrender bill, the surrender act, in the way that I did."
He argued the law would "take away the power of this government, and the power of this country to decide how long it would remain in the EU and give that power to the EU and that's really quite an extraordinary thing".
What is the Benn bill?
When Mr Johnson talks about the "surrender bill", he is referring to the European Union (Withdrawal) (No. 2) Act, also known as the Benn bill.
The act - which became law earlier this month - stipulates the prime minister will have until 19 October to either pass a deal in Parliament or get MPs to approve a no-deal Brexit.
Once this deadline has passed, he will have to request an extension to the UK's departure date to 31 January 2020 from the EU.
If the EU responds by proposing a different date, the PM will have two days to accept that proposal. But during this two-day period, MPs - not the government - will have the opportunity to reject the EU's date.
MPs on Thursday debated an urgent question over "the use of language" during Wednesday's ill-tempered debate.
Speaker John Bercow began the day's proceedings, by asking MPs from all sides of the house to temper their language and to "treat each other as opponents, not enemies".
In the heated debate that followed, several MPs said the prime minister should apologise for saying the best way to honour Jo Cox, the MP murdered during the EU referendum campaign, was to "get Brexit done".
Labour MP Jess Phillips said saying sorry would be the "bravest" thing for Mr Johnson to do.
Shadow cabinet office minister Cat Smith compared the language being used to that of drill artists, a type of rap which has been linked to gangs and violence.
"How are we as politicians in any position to accuse drill artists of glorifying violence when politicians themselves are not held responsible for the violent language they use and the impact it has on the culture and climate of debate?" she asked.
MPs also detailed some of the threats they had faced, with Tory MP Caroline Noakes describing how someone called her a "traitor who deserved to be shot" on a walkabout in her constituency.
Meanwhile, the longest-serving male and female MPs in the Commons - Ken Clarke and Harriet Harman - have asked for a Speaker's Conference, or meetings chaired by the Speaker, to discuss threats to MPs.
Cummings: 'Not surprising' voters are angry
MPs returned to Parliament on Wednesday, following the Supreme Court ruling that the prorogation of Parliament was unlawful.
Labour MP Paula Sherriff said she had received death threats which often quoted the prime minister's words, including "surrender act", and called on him to moderate his language.
In response, Mr Johnson said: "I have to say, Mr Speaker, I've never heard such humbug in all my life."
The prime minister also later said: "Believe me: the best way to ensure that every parliamentarian is properly safe and to dial down the current anxiety in this country is to get Brexit done."
Speaking at a book launch on Thursday evening, the prime minister's adviser Dominic Cummings said it was "not surprising" that some voters were angry.
"The MPs said we will have a referendum, we will respect the result and then they spent three years swerving all over the shop," he said.
"In the end the situation can only be resolved by Parliament honouring its promise to respect the result."
Mr Cummings - who was the campaign director at Vote Leave - also attempted to paint a picture of calm at No 10, saying: "This is a walk in the park compared to the referendum."
'Defiance of Parliament'
Meanwhile, Rachel Johnson, the prime minister's sister, told BBC Radio 4's World at One that her brother was using the Commons as a "bully pulpit".
Ms Johnson, who stood for pro-European party Change UK - which has since altered its name to The Independent Group for Change - in June's European elections, added: "It's not the brother I see at home. It's a different person."
Elsewhere, former Conservative prime minister Sir John Major has criticised Mr Johnson and warned that a "general election would solve nothing" in the Brexit crisis.
Mr Johnson has been calling for an early general election, but under the Fixed-term Parliaments Act he needs the support of two-thirds of MPs. He has twice failed to achieve this.
Speaking to the Centre for European Reform, Sir John said an election "would merely fuel the current feeling of disillusionment and disunity".
He also said he feared the government would seek to bypass the Benn Act, by suspending it until after 31 October when the UK is set to leave the EU.
He said he thinks they will do this by trying to pass an Order of Council, which can be approved by Privy Councillors - government ministers - without involving the Queen.
"I should warn the prime minister that - if this route is taken - it will be in flagrant defiance of Parliament and utterly disrespectful to the Supreme Court," he said.