"We're disappointed by the reaction to it. You must respect he has an opinion. He was being honest. He wanted to make a point. Whether he did that in the right manner is open to debate."
Allardyce pointed to statistics to prove his side are not dirty - Rovers are currently fourth in the disciplinary table having amassed 11 bookings and no red cards this season.
"It should go out there what the real facts are. The statistics back it up," said Allardyce.
"We don't feel the need to be publicising every day where we are in the Fair Play table but when somebody throws an allegation at you like that you have got to defend it.
"I think I've reduced the bookings ratio to about one and a half a game from just over two under previous managers and our sending off ratio is very, very good indeed.
"In fact the whole of this calendar year we have only had one player sent off in the Premier League which was Chris Samba at Stoke and all those that were there knew he shouldn't have been sent off in that game.
"So we're not going out to try to injure players and we take great exception to anybody that suggests that.
"We are physical when we need to be but we don't play dirty and never have."
Asked if Murphy should apologise, Allardyce said: "If he's man enough that's what he should do, yes."
Earlier this month, Murphy suggested Blackburn, Stoke and Wolves were adopting overly physical tactics to prevent other teams playing, and that such an approach was resulting in "ridiculous" and "brainless" tackles.
Allardyce claimed Murphy's assertions reinforce a public view of him and his side that is not true.
"The perception of Blackburn Rovers is the wrong one, in many, many cases and we have to live with it," said Allardyce. "The perception of Sam Allardyce is the wrong one, but I have to live with it.
"I don't quite know why he said it, you would have to ask him that, but it created a huge stir around the media world for a few days.
"We have to say he's nothing but completely wrong in his suggestions regarding Blackburn Rovers being anything other than good professionals who do the job honestly and who are committed.
"We never do that as a football club, I don't do it as a manager and the players certainly don't do it as professionals and I think everybody takes a dim view of what was said."
Meanwhile, Stoke boss Pulis continued: "One challenge on Hatem Ben Arfa by Nigel de Jong of Manchester City recently led to a broken bone.
"Another by Joe Cole, one of our technically most gifted players, resulted in a sending off for one of the most celebrated clubs in the country in Liverpool.
"How ironic is it that Danny Murphy chose not to discuss either challenge or manager in respect of those tackles? How selective can someone be?
"The game is cleaner today in terms of bad tackles than it has ever been. We must guard against rash tackles. However, we must also be realistic in that we will never completely eradicate injuries in a contact sport."
There have been a number of high-profile incidents involving players being injured by tackles this season.
On 11 September, Murphy's Fulham team-mate Bobby Zamora suffered a broken leg in a challenge by Wolves' Karl Henry, who was also fined two weeks' wages by his club following his tackle on Wigan's Jordi Gomez last Saturday.
Cottagers boss Mark Hughes criticised Stoke's Andy Wilkinson for a reckless tackle on Moussa Dembele in the Carling Cup.
And Newcastle's Ben Arfa will also miss most of the season after breaking his leg in a challenge by De Jong during Sunday's 2-1 defeat at Manchester City.
Puzzled Wolves manager Mick McCarthy added: "I've only had one conversation with Danny Murphy and that was after the Fulham game when he said 'don't worry, I'll make sure Zamora knows it was a fair tackle' and I said 'great'.
"If Danny Murphy can decide on, or analyse, my team talks or beliefs from that one 30 second conversation, then he is a better man than me.
"I find it incredible coming from someone who has never been in the dressing room with me, has never worked with me. Apart from that 30 seconds, we have never had a conversation."
Blackpool manager Ian Holloway also joined in the criticism of Murphy: "He'll have to face the music because I think he's totally wrong. Does he know what it's like to be a manager?
"I've never heard any manager who I've played for tell me to go out and tackle someone and hurt them and break his leg. I think it's a total insult to Tony Pulis, Sam Allardyce and Mick McCarthy."
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