"Tom's comments were inappropriate and they inflamed the situation and we're very disappointed with what he had to say," Nisbett said. "Unfortunately they were made.
"You'd like to think that when you make those comments you try to take out the emotion of the situation. It's very difficult to do that but you also need to be extremely accurate if you're going to make comments like that.
"Some of those inflammatory comments by some people just are unwarranted."
Nisbett said Gaff was "beside himself with what happened" and he cast a shattered figure on the bench after the incident even as coach Adam Simpson tried to console him.
Making matters even more awkward for the midfielder is his close relationship with the Brayshaw family. He's become good friends Andrew because of his bond with Hamish Brayshaw, who the Eagles drafted last year but is yet to make his senior debut.
Simpson also played footy with Mark Brayshaw, Andrew's father, who has spoken to Nisbett and his former teammate about the drama.
"I think five days ago the (Brayshaw) brothers and Andrew Gaff were on the golf course together so it's an extraordinary situation we all find ourselves in at the moment," Nisbett said. "I think it's a genuine friendship.
"Kids come through the system all the time and it wouldn't surprise you that with Hamish at our club there is a reasonable relationship there.
"I've known Mark for a number of years and it wasn't an easy conversation."
Gaff will front the AFL tribunal this week and many predict he will cop a ban ranging from six to eight weeks.
The controversy has also intensified the debate over whether the AFL should introduce a red card for similar offences. Nisbett refused to speculate on what sort of punishment Gaff should cop, saying the club needed to wait for the AFL's disciplinary process to play out, but strong comments he made three years ago about the need to rid footy of thuggish acts resurfaced today.
In 2015 Nisbett said: "Guys don't sign up for this and if you're going to go outside the laws of the game, you should be punished with the maximum penalty.
"Enough is enough. This has been creeping in for a number of years. It's not so much the number of incidents but their severity."
The footy world has been quick to condemn Gaff for his brain explosion and AFL icon Leigh Matthews said the 26-year-old would have to live with the shame of his unprovoked attack for the rest of his life.
"I've been in both those situations — I've been Andrew Gaff and I've been Andrew Brayshaw where I've been splattered by another player — Andrew Gaff is the one who's going to be mortally wounded for the rest of his life," Matthews said on Macquarie Sports Radio.
"Brayshaw will be uncomfortable for a week or two and then he'll be fine.
"But the guilt and the shame will live with Andrew Gaff for the rest of his life.
"This was a really bad split-second decision that Andrew Gaff made and you've got to get penalised.
"If you talk about who's going to suffer for most of their life, I guarantee you Andrew Gaff's going to be a lot more in that category than young Brayshaw will be once he's recovered over the next week or two or three."