Glenn Sterle, chairing a hearing on regional affairs, directed the sexist comment at Nationals senator Bridget McKenzie at a heated Senate estimates hearing on Tuesday.

The Senator for WA has been blasted by both sides of the aisle, with one Labor colleague describing the remark as "completely unacceptable in the modern age".

Senator Sterle threatened to "do my block" after Senator McKenzie attempted to speak over a witness, a common occurrence in the often-contentious hearings.

"Senator McKenzie, do you always have to have the last word? I was going to defend you then," he said.

"Honestly, like a naughty little girl. Just be quiet while someone finishes. You don't have to have the last word!"

An hour after the comment, and having initially refused to withdraw it, Senator Sterle claimed the "outburst" was "not like me".

"I've reflected on my words earlier today, and Senator McKenzie I want to apologise for my outburst, there is no excuse for the language I used ... I'm not dodging it, it was out of order," he said.

Earlier, the comment immediately raised the ire of Greens senator Peter Whish-Wilson, who demanded Senator Sterle withdraw.

Senator Sterle initially refused to listen to his objections, before telling Nationals senator Matt Canavan he was "really stretching the friendship" when he attempted to intervene.

"No, I don't care. You're all as bad as each other ... I will not withdraw it because I am probably one of the ... easiest to get along with," Senator Sterle said.

An apparently exasperated Senator Sterle eventually did apologise after Senator McKenzie raised the comment.

"Yes well, I'll take that back. You're not a naughty little girl. I apologise. Now, do you want to ask your question?" Senator Sterle said.

Prime Minister Anthony Albanese pledged to improve the culture of Parliament, after the Jenkins review found evidence of widespread bullying and harassment.

Emergency Management Minister Murray Watt, who was appearing before the committee at the time, described it as an "extremely unfortunate remark which should not have been made".

Senator Watt did not criticise his colleague at the time, but claimed he had pulled Senator Sterle aside to discuss the matter and he was "remorseful".

"What Glenn said was completely unacceptable in the modern age," he told reporters.

"It's utterly unacceptable for those kinds of remarks to be made in any workplace environment or in society as a whole.

"[But] I'm pleased that Glenn pretty quickly made an apology and recognised he'd done the wrong thing."

Coalition spokesperson for women Sussan Ley accused Labor of hypocrisy.

"In the same week that Labor used the passing of laws recommended by the Respect@Work report to call for more respect for women, one of their Senators called one of my colleagues a 'naughty little girl' in Senate estimates," she said.

"It is unacceptable and needs to be called out.

"Is this the respectful workplace Anthony Albanese promised us?"

Minister for Women Katy Gallagher also labelled the remark "unacceptable".

"He's done the right thing by publicly apologising to Senator McKenzie," she said.