Murphy claimed last week that players are being injured because certain managers are sending their teams out too fired up, with the Potters one of three clubs - along with Blackburn and Wolves - that he named specifically.
His comments have created a storm and after Blackburn manager Sam Allardyce yesterday challenged Murphy to publicly apologise for the remarks, Pulis has now had his say on the matter.
Reading a statement aloud at today's press conference, Pulis said: "Two challenges this season have been committed by top players who represented their countries at this summer's World Cup.
"One challenge on Newcastle's Hatem Ben Arfa by Nigel de Jong of Manchester City recently led to a broken bone.
"Another by Joe Cole, one of our most technically gifted players, resulted in a sending off for one of our most celebrated clubs in the country, Liverpool, who are currently managed by Roy Hodgson, someone I have great respect for.
"Even the technically best players are prone to making mistimed challenges. But have they really been sent out to hurt a fellow professional? I don't think so.
"How ironic it is that Danny Murphy chose not to discuss either challenge or manager in respect of those tackles. How selective can someone be?
"Maybe Murphy's pursuit of a new career in the media does not allow him to criticise, or fall out with the Premier League big boys.
"Instead, in my opinion, he has selected easy targets that are based on his own perception and not facts."
Pulis, like Allardyce, also feels Stoke are wrongly lambasted as a dirty team and pointed to the Premier League Discliplinary table to prove his point.
He added: "We currently lie seventh in the league and are 10th in the Disciplinary league.
"If you add that to last season we are currently joint 10th alongside Arsenal, which is quite a feat considering we spend a great deal more time without the ball than they do. This is not fabricated, this is fact.
"I firmly believe the game is cleaner today in terms of bad tackles than it ever has been before, but I wish I could say the same thing in terms of other ills such as simulation.
"Tackling is an art form and we must never take it out of our game, no matter how much is suits certain players and certain clubs.
"To do so, in my opinion, would destroy what makes the Premier League and English football in general so fantastic.
"We must guard against rash tackles, whether committed by most gifted players or just a mere mortal. However, we must also be realistic that we will never completely eradicate injuries in a contact sport."