"The difficulty is they can't make MediaWorks make long-form current affair programmes.
"It can make whatever programmes it wants to make, but what it can't do is treat employees unfairly," she said.
Clark said a historic focus on news and current affairs by TV3 had contributed to current tensions between staff and management.
"[TV3] took it upon itself, under its previous management, to be the quasi-public broadcaster. And that created expectations," she said.
News of the rebellion by 3D staff was broken this morning by website The Spinoff, but sources inside MediaWorks have independently confirmed the existence of the dispute to the Herald.
A spokesman for MediaWorks said they were unable to comment on the matter.
In the early evening of November 4 MediaWorks put out a three-paragraph media release announcing the show was being considered for closure.
Group head of news Mark Jennings said in the statement: "Long-form current affairs in challenging to make commercially viable all over the world."
Staff were given a week to present proposals to save the show, with that deadline understood to have since expired.
The Spinoff reported the challenge by 3D staff alleges MediaWorks did not consult in good faith, provided misleading and inaccurate reasons for the change, and the week-long consultation process was inadequate.
The show is the last-standing long-form current affairs show screening on TV3, and this year had received $567,420 in NZ on Air funding to support 10 pieces of investigative journalism.
3Ds small crew of journalists and producers played a key role in exposing the shoddy police investigation into the 1992 rape and murder of Susan Burdett.
The saga resulted in Teina Pora being freed, and his convictions quashed, after 21 years in prison.
MediaWorks has had to endure a stormy 2015, with poor ratings for a number of reality shows seeing local versions of Masterchef and X-Factor canned.
Its news division is undergoing similar turmoil, with long-running current affairs showCampbell Live shut down in May and the company's news divisions centralised earlier this month under the new Newshub banner.