It said the tone of his comments on the National Prosecuting Authority's (NPA) consideration of representations on Zuma's case indicated he was "either knowledgeable of the decision or seeking to pre-empt an outcome that is favourable to Jacob Zuma".
This, the party said in a statement, was "tantamount to him undermining the independence of the NPA and the judiciary which is unfortunate for a person of this stature".
The comments they were responding to were made at a book launch in Durban on Wednesday night.
While the ANC leader was a warm and friendly man, Tutu said he was not the ideal president.
"In the year of [US President Barack] Obama, can you imagine what it is like when you are walking in New York and they ask you who will be the next president?"