Two asylum seekers found in the Torres Strait spent Sunday night in the Thursday Island police station.
The Immigration Department said the men, claiming to be Somalis, were found by Customs and Immigration officers on Boigu Island on Saturday morning.
The ABC reports the department said they were likely to be transferred to either Nauru or Manus Island in Papua New Guinea.
AAP reports Immigration Minister Tony Burke said they will be treated no differently than others arriving by boat in Australian waters.
"They are now discovering that the rules that apply to them are identical," Mr Burke told ABC Radio on Monday.