One of the deleted paragraphs referred to an "embarrassing public spat" between the minister and Canadian Judge Ian Binnie, who had considered Mr Bain's compensation case.
A spokeswoman said: "These two actions were the only two made - and both [were] completely transparent and in accordance with Wikipedia policy. No further edits."
The Government did not have any rules regarding MPs or their staff editing Wikipedia.
The website does not allow people with a conflict of interest to edit articles, and the press secretary was warned by the site's administrators.
But the warning was withdrawn because the conflict was clearly signalled on the site and the press secretary had not made any further changes to Mrs Collins' page or other related pages.
Mr Brooking said that another contributor, whose identity was not known, had heavily edited or removed a number of critical references to Mrs Collins in her current and previous portfolios.
Mrs Collins' spokeswoman said that these changes did not come from the minister's office.
She also noted that Mr Brooking had been banned from Wikipedia for using more than one account.
Mr Brooking said he had been blocked from the website for creating new accounts to get around the ban.
However, he remained concerned that pages relating to the National-led Government were being "sanitised" online.
"Ninety per cent of what I've written has been deleted. Most of these pages have been sanitised and they convey a very distorted picture of the current situation in New Zealand."