"I had a cold last week and am still coughing which got me on the run,'' Brown said.
"Still I am very happy with second place today and I will definitely be back next year.''
Harper, the 2010 age group Ironman world champion, enjoyed a strong 53.00 swim and excellent bike of 5:00.37 to find herself pushing clear of the pack but five minutes down on former Ironman Australia champion Rebekah Keat after the 180km ride. She had a margin of nine minutes over the closest chasers, Australians Carrie Lester and the experienced Belinda Granger, with Hammond a further six minutes back.
Harper found herself in the lead after Keat withdrew with a calf strain at the 5km mark. Harper began to tire in the heat as Lester began to close the gap, eventually passing the New Zealander with 11km remaining.
Lester won in a 9:21.00 with Harper holding on strongly in 9:22.34 while Hammond produced the best marathon of the day, with her impressive 3hr10min effort in the heat meaning both Kiwis enjoyed their first Ironman podium placings.
Earlier seven-time Ironman New Zealand champion Joanna Lawn finished third in the Ironman 70.3 race.
Results, Cairns Airport Ironman:
Men: David Dellow (AUS) 8:15.04, 1; Cameron Brown (NZL) 8:22.21, 2; Jimmy Johnson (AUS) 8:29.36, 3. Also: Simon Cochrane (NZL) 9:02.01, 8;
Women: Carrie Lester (AUS) 9:21.00, 1; Belinda Harper (NZL) 9:22.42, 2; Candice Hammond (NZL) 9:24.45, 3.