Speaking to the BBC, Harry Arnold said that he had written the story in a "fair and balanced way", noting that the controversial claims were just "allegations".
He also revealed that it was Kelvin MacKenzie, The Sun's editor at the time, who wrote the headline: "The Truth".
The Sun's article alleged that the 1989 disaster followed "mass drunkenness" among Liverpool supporters, and claimed that some fans had urinated on police and picked victims' pockets as their bodies lay on the pitch. The paper said that the allegations had come from unnamed South Yorkshire police officers.
Official papers are to be released next Wednesday on the tragedy 23 years ago, in which 96 people lost their lives.
Interviewed for the documentary Hillsborough: Searching for the Truth, Arnold says: "On The Sun, Kelvin MacKenzie was the rather controversial editor at the time, he liked to write his own headlines.
"He wrote the headline 'The Truth', and the reason I know that is I was about to leave the newsroom when I saw him drawing up the front page."
He continued: "When I saw the headline 'The Truth' I was aghast, because that wasn't what I'd written.
"I'd never used the words the truth, 'This is the truth about the Hillsborough Disaster'. I'd merely written, I hoped and I still believe, in a balanced and fair way.
"So I said to Kelvin MacKenzie, 'You can't say that'. And he said 'Why not?' and I said 'Because we don't know that it's the truth. This is a version of 'the truth'.
"And he brushed it aside and said, 'Oh don't worry. I'm going to make it clear that this is what some people are saying'.
"And I walked away thinking, 'Well I'm not happy with the situation'. But the fact is reporters don't argue with an editor.
"And in particular, you don't argue with an editor like Kelvin MacKenzie."
MacKenzie has not yet responded to the BBC's request for comment.
But he discussed the Hillsborough article on the BBC's Daily Politics show last December. Asked if he regretted the headline, MacKenzie replied: "Probably, yes I do."
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