Read more: One on one with a bomber pilot, fearless under fire
"He passed away in the early hours of this morning after a very short illness," Mr Munro said.
"His family had been spending time with him, and we're sorry to see him go. He was the patriarch of the family but he went very peacefully and for that we're very pleased."
His father was 96, Mr Munro said, which was "an incredibly long life given what he's had to go through".
"We're sorry to see him go, we're very distressed. [But] we're realistic that it was time for him to pass. And he went the best way - quietly."
Mr Munro died following heart problems, the New Zealand Bomber Command said.
In a tribute to the World War II veteran, the association described him as a patron and a good friend.
Our sincere condolences and with deep sadness to Les Munro's family. He showed us what a true gentleman and hero is all about.
"I have extremely sad news. Our New Zealand Bomber Command Association Patron, and well known Dambuster pilot, Les Munro passed away last night following a spell in hospital with heart problems," a tribute post on its Facebook page said.
" So, so sad. he was a mighty man."
Peter Wheeler, chief executive of the New Zealand Bomber Command, posted: "A good mate and a real loss to all of us. Godspeed my friend."
Others also paid tribute to the former pilot.
Andrew Porrelli said: "Our deepest condolences to his family and friends, from all the Veterans, admin, family and friends at 514 Squadron RAF - Rest in Peace Mr Munro Sir!!"
Brett Curtis described the death as "exceptionally sad news", and shared this personal memory of meeting Mr Munro: "Had the opportunity to spend 5-10 minutes with him at Tauranga Air Show a cple of years ago - when I mentioned that he was flying so low the German gunners could have thrown stones at his plane, he replied 'Sure sounded like it, son!' As I'm in my 50s, it's been a long time since someone called me 'Son'! But I had so much respect at meeting Les Munro I was still bouncing around with an adrenilin rush for hrs - not often you meet a true Hero!"
Earlier this year Mr Munro gifted his gallantry medals, along with his flying log book and other memorabilia, to the Museum of Transport and Technology (Motat), after they were saved from auction by British businessman and World War II enthusiast Lord Ashcroft.
Mr Munro said at the time he had felt compelled to put his treasured war memorabilia up for auction to raise money to help with the maintenance of the Bomber Command Memorial in London after visiting the site in 2013.
His medals and memorabilia were set to go under the hammer at London auction house, Dix Noonan Webb, before Lord Ashcroft stepped in and offered to donate 75,000 pounds ($150,000) to the fund.
Mr Munro was also this year awarded the French Legion of Honour for his bravery and commitment in World War II, adding to his list of honours.