The 12-year old was snatched by the crocodile while swimming with friends in a water hole in Kakadu National Park, in the Northern Territory.
Rangers said neither of the two crocodiles appeared to be the attacker, and that the search would continue.
Another boy was also mauled by the crocodile, but managed to escape.
Australian police searched overnight for the crocodile and the seized boy.
They said that two crocodiles, one measuring 4.3m (14ft) and the other 4.7m (15ft), had been shot and examined in the course of their search.
"We've since had a look at both crocodiles and neither of them had anything in their stomachs," Sergeant Stephen Constable said.
"We're going to continue the search today," he added.
Officials say visitors are warned not to swim in Kakadu's watering holes because of the risk of crocodile attacks.
Saltwater crocodiles can grow up 7m (23ft) long and weigh more than a tonne. They are a common feature of Australia's tropical north.
In August, a man was killed by a crocodile as he swam in a river in the north during a birthday party.
Australian police have shot two crocodiles dead in a search for a missing 12-year-old boy attacked by a crocodile on Sunday.