Her departure is the second high-profile casualty at TV3 in the past year after John Campbell left in May when his show Campbell Live was dumped.
The Weekend Herald can reveal Barry, who has been with the company since 1993, resigned on Thursday. There is speculation she is headed to rival broadcaster TVNZ.
The shock move is the latest drama to rock TV3's news and current affairs department in the last 18 months. It is understood Barry's departure has caused turmoil at the broadcaster, which has merged its television and radio newsrooms.
Barry is a lynchpin at both ends of the day for the company. She co-stars on the Paul Henry breakfast TV and radio programme and is an anchor on the 6pm news.
She is immensely popular among MediaWorks staff and the public, and her colleagues are said to be devastated she is leaving.
A TV3 spokeswoman confirmed last night that Barry had resigned.
Paul Henry, asked last night for comment, appeared to be momentarily speechless.
After a palpable pause he eventually said: "Er ... I don't have any comment to make. Thank you and good evening."
Barry (46) as not been on air for some days. Her replacement evening newsreader Melissa Davies tweeted on Thursday: "Both Hilary and Mike [McRoberts] are sick. Wish them well."
She went on to say she hoped she wouldn't catch "whatever's around the studio".
Sources told the Weekend Herald there had been some internal debate about how her departure should be managed, particularly given a major announcement on the company's future had been scheduled for Tuesday.
It is understood MediaWorks boss Mark Weldon is overseas on business and wanted to be back before the news was made public. However, staff began to learn of Barry's departure yesterday.
Weldon has cut a controversial figure since joining MediaWorks as chief executive in August 2014.
The former Olympic swimmer and NZX chief executive turned wine-maker has been under scrutiny amidst concern over ratings at TV3.
Under his stewardship MediaWorks ditched Campbell Live last year sparking a heavy public backlash. That was followed by the decision to axe another current affairs programme 3D, hosted by Samantha Hayes. In the aftermath journalists including Paula Penfold - who is married to Barry's 6pm co-host Mike McRoberts - also left.
It is understood Barry has been dissatisfied with the network's direction for some time.
One source told the Weekend Herald that if Barry did join arch-enemy TVNZ, where she is believed to be in talks, it would be a "double whammy" for rival TV3. It is not known what role she could take up at TVNZ, but one source said Barry only had to serve a month's notice at TV3.
Barry presented 3 News on weekends for six years, before fronting the flagship weeknight news programme.
She recently celebrated her 11th TV3 news anniversary alongside NewsHub co-presenter Mike McRoberts.
Last year she also became news anchor for the morning Paul Henry Show.
She and husband Mike Barry, a teacher and son of All Black Kevin Barry, have two sons, Finn and Ned.
In February Barry made the news herself when she laughed uncontrollably while delivering a report on the morning programme after reading an item about a former Malaysian diplomat who admitted going to a young woman's home with no pants on and defecating on her step before leaving.
MediaWorks owner, vulture fund Oaktree Capital, has been taking a closer interest in its New Zealand broadcaster recently. Earlier this month it appointed one of its bankers to the board, and it passed a new constitution which sets a $2 million annual limit on any new investments, liabilities or litigation by Weldon and his team that has not been approved by directors.
