"Cosatu has not made a 'dramatic change of tone', or 'turned on' the deputy president of the ANC, as alleged in the article," said the union's secretary-general Zwelinzima Vavi.
"There is no change in our position. The federation has always said that in relation to the rape trial that the law must take its course, and that remains our view."
A front page headline in a daily newspaper on Friday read: "Cosatu turns on JZ".
Vavi said journalists had only taken into account his comment that Zuma should pay if he is found guilty, and ignored calls that the media should accept a possible not guilty verdict.
The report quoted Vavi as saying: "In this particular case, we say justice must take its course. If he is guilty, unfortunately he has to pay for that. If he is not guilty, he must go back to his life, back to his positions."
Vavi says he was correctly quoted
Repeating this sentiment, Vavi said he was merely pointing to some of the consequences which would inevitably follow a guilty verdict, if that were the outcome of the trial.
The story read: "He [Vavi] tacitly hinted that support for Zuma was waning within the labour movement".
It also said the union had made an "about-turn" on its view of Zuma as a friend of the workers.
Vavi said he had been correctly quoted, but his statements were in response to suggestions that Cosatu supported Jacob Zuma on the basis that he was a "left-wing socialist on whom we would depend to take forward our struggles".
'Zuma's defence was a matter of principle'
Vavi said wanted to clarify that this was not necessarily the case.
"Cosatu has never opportunistically supported Jacob Zuma because he is a champion or messiah who would deliver left policies to workers and the poor," said Vavi.
He said the federation had come to Zuma's defence as a matter of principle.
"We could not allow a person with his stature to be treated in the manner that he has been treated," he said
Cosatu would be guided by its historic position on the question of rape which, said Vavi, the union views in the "most serious light".
Cosatu urged South Africans, in particular the media, to respect the outcome of the rape case.