ECB chief executive David Collier told BBC radio on Sunday that Pietersen's texts to South African players during the recent Test series were in response to messages from the opposition.
"This is absolute rubbish," CSA's acting chief executive Jacques Faul said in a statement on Monday. "What is particularly disappointing is that I had a face-to-face meeting with Mr Collier when I was in London for the Lord's Test.
"He did not raise this allegation with me then and I would have thought as a matter of courtesy and decency he would have spoken to me about it before going public in the media."
South African-born Pietersen was dropped for the third and final Test at Lord's and Collier alleged the text row was part of a tactical masterplan by the visitors who won the series 2-0.
"These texts were responses to messages from certain members of the South Africa team and I would not condone an England player doing it if it was the other way around and I certainly think they provoked the situation," said the ECB chief.
"I think there was a tactic which was used. I think that is sadly some of the ways of modern sport."
Faul, however, criticised the way England's cricket officials had handled the whole situation.
"This is not the way CSA goes about its business and it is not the way the ECB have done business with us in the past either," he added.
"It is very disappointing because in the past our relationships with the ECB have always been cordial and constructive.
"This is an internal ECB matter in which we do not wish to be involved. It served as a distraction to our players that we did not need during the Test series."