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The Commission - which does not have a Facebook page itself - first found out about the situation on Sunday, after users reported they were unable to share links to the government organisation's website.
It comes just after the social media giant resolved its week-long standoff with the Australian government over a proposed new law which would make Facebook pay to host news outlets.
A statement issued by Treasurer Josh Frydenberg said they would introduce amendments to the proposed law, which he said "will provide further clarity to digital platforms and news media businesses about the way the Code is intended to operate and strengthen the framework for ensuring news media businesses are fairly remunerated."
"The government has been advised by Facebook that it intends to restore Australian news pages in the coming days."
The ban was only meant to restrict publishers and people in Australia from sharing or viewing Australian and international news content.
But somehow, the Climate Change Commission was caught up in it all.
When a user attempts to post onto Facebook a link to the Commission's website, a box pops up which says: "This post can't be shared".
"In response to Australian government legislation, Facebook restricts the posting of news links and all posts from news pages in Australia. Globally, the posting and sharing of news links from Australian publications is restricted."
But the commission's communications manager, Fran Lovell, said it made no sense.
"The Climate Change Commission is a bit confused that Facebook has mis-identified us as an Aussie news site.
"Lots of people have been asking us what the story is and we are not entirely sure - but we can promise we have alerted Facebook to explain where Aotearoa is in relation to Australia.
They have not heard back from Facebook.
It comes at a busy time for the commission, which is in the middle of its engagement period over its Draft Advice, published just over three weeks ago.
They have made the decision to extend the engagement period by two weeks out to the end of March.
"Our consultation is really important and people should head to our website to learn more and make a submission," Lovell said.
Facebook has not responded to either the commission, nor to an RNZ request for comment.
It's not known if other government departments or agencies are also affected; or any other New Zealand-based news organisations.