Super Rugby's organising body also said that Cheika and Peyper had received written warnings about the incident.
But Sanzar says that Cheika entering the officials' room midway through a game to inquire about why certain decisions had been made did not constitute a breach of the tournament's code of conduct.
If Cheika is found guilty of breaching the code of conduct, he will be facing a six-month ban from all coaching after being handed a suspended sentence for abusing a cameraman last year.
The statement said Sanzar concluded the exchange between Cheika and Peyper was "short and polite" and confined to the coach seeking clarity about one specific scrum ruling.
The Herald was told that in this instance, the incident didn't meet the threshold to trigger a judicial hearing as Cheika was neither aggressive nor abusive and nor did he use foul language.
But the prevailing view in New Zealand is that using the break to enter the referee's room - regardless of intent or content - is a serious offence and should automatically be considered a breach.
Section 8.3 of the Code of Conduct clearly states: "All persons ... shall not engage in any conduct or any activity on or off the field that may impair public confidence in the honest and orderly conduct of a match."
The Herald spoke to several current and former persons with extensive Super Rugby match experience and none could recall a similar incident. All agreed that a coach having any kind of halftime dialogue with a match official would be a serious concern.
Sanzar's statement said: "There is no evidence that the referee was influenced by the exchange in his handling of the match."
The penalty count in the first half was 8-1 against the Waratahs. In the second half it was 9-1 in their favour.
The Herald also understands the Blues have multiple video clips to support their view the game was refereed one way in the first half and differently in the second.
Some of the confusion that arose from Sanzar's position was in regard to Sanzar's need to write warning letters to both Cheika and Peyper. The question was raised: if they were not guilty of doing anything wrong, why did they receive a warning letter?
There was further confusion about Sanzar's need to write letters to all Super Rugby coaches after the incident. All were reminded not to enter the referee's room at halftime yet Sanzar was adamant in its released statement that it is neither an offence or against the rules to do so.
