Asked whether he had warned the All Blacks about their behaviour he said: "I've given them a reminder that there is a certain way to behave."
The Chiefs launching an investigation, alongside New Zealand Rugby, following allegations of improper behaviour with a stripper at the team's season ending function earlier this week.
Speaking to Radio Sport's Martin Devlin, Flexman said the comments do not reflect his values.
"Having read the comment verbatim it was one thing that jumped out to me. It was a high pressure environment when I made the comment, and the context around making the comment is somewhat relevant.
"It certainly gives the impression that there are questions around her integrity given her vocation... I regret the way it's been phrased if I'm honest."
In a later press conference, Flexman said he was "really, really disappointed" a stripper had been hired and "did not condone" that decision.
He said an investigation would be launched immediately and "appropriate action" would be taken against players if the stripper's allegations were proved correct.
Earlier, Flexman had cast doubts on the credibility of the allegations. However, during the press conference he said "no assumptions" would be made before the investigation was complete.
The press conference was cut short as reporters asked questions including if any All Blacks were involved.
The scandal erupted after a stripper was booked by the team at their season-ending function at the Okoroire hot pools near Matamata.
She alleged the players touched her inappropriately during her performance.
The stripper, known as Scarlette, told Radio New Zealand it was an intimidating job and the players had no respect.
"I made it very clear that I didn't want to be touched, even though I had a smile on my face it doesn't affect the words coming out of your mouth - that was just me maintaining my professionalism, trying to get out of there safely," she said.
"I had one of the players going through my phone, they proceeded to lick me in places that I don't totally agree with. I felt like I was pressured for that."
She told Radio New Zealand that the incident should be investigated and disagreed with the Chiefs' view on events.
"Well then they weren't looking, were they? I mean, that's where it turns into a 'he said, she said' part of the argument which I believe is present in any case of sexual abuse, anything like that.
"If my word means nothing, then so does every other woman's word that's ever said anything against someone."
Flexman had said that the stripper's claims were "one person's accusation and her standing in the community and culpability is not beyond reproach".
He told Devlin the comment was "not consistent with who I am and my values".
"I'm not in a position to make that assertion because I don't know the woman from a bar of soap."
He agreed that he needed to apologise to the woman.
"Absolutely, the context is important for me but in terms of the way it's been phrased I regret it."
Flexman said the incident would result in an investigation into the organisation's culture.
"We expect better from our players and as an organisation. We are disappointed this has happened and we weren't made aware of the players' intentions.
"We'll be seeing if we need to ask some deeper and harder questions."
The allegations come after lock Michael Allardice apologised for chanting "here come the gays" and offending members of the public present at the pools.
