The 30-year-old looked relaxed while sitting on the 3.1m (10ft) crocodile, removed from a trap in Darwin Harbour.
The pictures, which also show him hauling in the catch, were released by the Parks and Wildlife Commission Northern Territory.
Meanwhile, the prince has completed an eight-day tour of New Zealand.
Wildlife ranger Erin Britton said the prince would make "a great croc catcher" and said he did a "great job" helping the crocodile management team in the removal of the crocodile.
Bess Price, minister for parks and wildlife, said it was a "top secret mission" that would leave "a unique lasting impression" of the Northern Territory with Prince Harry.
Rangers in the Northern Territory remove crocodiles from waterways used for boating and fishing to limit the risk of fatalities and injuries.
The Parks and Wildlife Commission Northern Territory says more than 200 crocodiles, common in Australia's tropical north, are removed from Darwin Harbour each year.
They are taken to crocodile farms or killed.
Meanwhile, on his final day in New Zealand, Prince Harry scored a winning goal in the dying seconds of a football match to the delight of a cheering crowd.
The prince took part in the five-a-side game with a group of young players to promote the Fifa under-20 World Cup.
After the 8-7 victory in Auckland, he said: "I've had a great time and that win was so well-scripted, thank you."
Prince Harry has spent a week in New Zealand, his first visit to the country.
New Zealand Prime Minister John Key, who was made team coach, praised the prince's "great display of athletic ability and sheer presence".
"If you want a spot in the New Zealand team, call us any time, it's yours," he said.
Prince Harry also talked to his teammates about football and asked if there were any fellow Arsenal fans.
When one boy said he supported Stoke City, the prince said: "I wouldn't have spoken up if I was you."
Prince Harry also revealed he was looking forward to the FA Cup final between his team, Arsenal, and brother Prince William's side Aston Villa.
He then went to the AUT Millennium Institute of Sport and Health where he tried out different exercises with All Blacks rugby player Kieran Read.
These included lifting weights, playing netball, throwing a rugby ball through a tyre and rope pulling.
Prince Harry landed in the country on 9 May, receiving a traditional Maori welcome in Wellington before travelling to Stewart Island, the country's most southern and remote community.
He has also spent time in Christchurch, finding out about the city's efforts to regenerate after the earthquake in 2011.
Prince Harry helped capture a saltwater crocodile during his tour of Australia last month, newly-released pictures have shown.