Mr Paterson says it is not an unusual move, and similar things happened under the previous government.
He says he does not support the view that statutory authorities are independent "for all purposes", rather independent for specific purposes "for which they were created".
He denies the directive requires the institutions to have their material vetted by the PM’s office.
"It doesn’t need to be vetted, and there’s no suggestion in the language that was used or any language that I’ve used to suggest that something was being vetted," he said.
"This is not about constraining academic observation or comment in an independent area, this is not about independent commentary from scientists, this is about institutional media releases.
"It’s about ensuring a consistency in message."
Mr Paterson says the move allows the Government to be aware of what is being published.
"If you’ve got key themes that a Government has gone to the people on in critical areas in terms of its platform, it is not surprising, it is unexceptional that a government would want to be aware of a message that was being put out," he said.
"We were being asked by these agencies for guidance and we’ve provided that guidance to the individuals.
"It’s written in reasonably relaxed language, it’s not a directive. Some of the facts in the stories that have been published this morning are not accurate and clearly one of the agencies that we provided that guidance to has passed it straight on to the press."