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It is understood an email went out to TVNZ staff today from head of current affairs Paul Yurisich to say he has accepted the resignation.
In a statement, the network told the Herald, "TVNZ has accepted the resignation of Breakfast presenter Kamahl Santamaria. Kamahl has been on leave the last week, while he dealt with a personal matter which required his full attention, and he has now advised that he wishes to take an extended break with his family.
"Kamahl is focussed on his family at this time, and we ask that everyone respects their wish for privacy."
Yesterday the Herald reported that the new star had not been seen on Breakfast for nine days. Santamaria was last seen on the show on May 18.
When contacted by the Herald for comment yesterday, TVNZ issued a short statement revealing Santamaria is currently navigating a "family emergency".
A spokesperson from the network said, "Kamahl is currently away dealing with a family emergency."
They added: "The matter is private to Kamahl and we are respecting he and his family's privacy."
TVNZ are yet to confirm who will fill in for Santamaria on the morning news show.
Santamaria confirmed in April he would be officially joining TVNZ's Breakfast team after John Campbell took on another role as TVNZ's chief correspondent.
The former Al Jazeera news anchor shared his excitement on Twitter at the time after TVNZ revealed he would be joining Indira Stewart, Matty McLean and Jenny-May Clarkson at the Breakfast table.
"It's official ... I'll be joining the @Breakfaston1 team later this month!" he wrote.
"Looking forward to early starts, the unpredictability of live breakfast TV, and hanging out with Jenny-May, @MattyMcLean & @Indiratweets every day."
Santamaria, an Auckland-born journalist, started his career as a sports reporter for Newshub before leaving New Zealand to pursue other ventures.
He had been teasing the announcement on Twitter after revealing he was leaving Al Jazeera, where he worked for over 16 years.
He told viewers, "Finally this half-hour we are always taught as journalists not to make the story about ourselves but it would be remiss not to mention that today has been my last day at Al Jazeera after nearly 16 and a half years.
"It has been the most extraordinary journey, surrounded by exceptional journalists telling the stories which matter. I am so proud to have been a part of this channel and I will miss it greatly."