The 22-year-old, who made the world athletics championship final won by compatriot Tom Walsh earlier this year in London, is suffering from myocarditis and been advised to avoid training for at least six months.
"With careful management he should be able to return to training and competition in the latter half of 2018," Athletics New Zealand said in a statement.
The recovery period would rule him out of the world indoor championships in Birmingham from March 1-4 and the Commonwealth Games, which will be held on Australia's Gold Coast from April 4-15.
Myocarditis, which causes inflammation of the heart wall, is caused by a virus.
Gill, who usurped Jamaican great Usain Bolt as the sport's youngest world junior champion in 2010, told local media he had been woken up in the middle of the night two weeks ago with chest pain and rushed to hospital.
"I was lost for words when I got those results. It was a shock," Gill told the New Zealand Herald. "I wasn't really expecting anything but I wanted to get it checked out just to be safe.
"To have significant heart damage at my age is a bit worrying but there are other high performance athletes it happens to. It's just bad luck. It's been a bit of a shock these past two weeks.
"It's disappointing I can't prove myself at the Commonwealth Games next year but in four years' time I'll be able to give it a good crack.
"I was in really good form so I'm disappointed I can't challenge for that gold medal but I'll be back in 2020 (for the Tokyo Olympics) and the 2019 World Championships."
(Reporting by Greg Stutchbury; Editing by Toby Davis)
