Torres Strait Islands Regional Council mayor Fred Gela expects to see growing numbers of asylum seekers going through the area in an attempt to reach Australia.
Two men claiming to be Somali asylum seekers arrived on an island in the strait on Saturday.
''Coming through (Papua) New Guinea undetected, that is very easy to do," Mr Gela told the ABC. "I want to be brutally blunt about this, this is the first wave of many to come."
The Queensland government has also warned that the federal government's PNG asylum-seeker deal could lead to the Torres Strait becoming a new route for people smugglers
The federal government's plan to send all new asylum seekers to Papua New Guinea was supposed to stop the boats.
The ABC reports the Torres Strait is only 4km from the mainland of PNG at its northernmost point and the frontier has been a well-known smuggling route for drugs, guns and people for years.
However, the remote and sparsely populated islands are difficult to monitor. Two federal government officials greet any arrivals, record names, and look over cargo for signs of pests and disease at the boat ramp on Boigu, the northernmost island.
Nearly all visitors are from across the water in PNG, about 7km away.
Owing to centuries-old family links, the Australian government allows villagers from 13 settlements along the PNG coast free movement in the region, and they make the trip every week to bring their goods to market.
"Boigu and Saibai are sort of the doorway for internationals to come in,'' said regional council representative Dimas Toby. ''We've had (arrivals) in the past that came through here as individuals and a group."
No weakness in border protection
However, the ABC reports Home Affairs Minister Jason Clare denies there is weakness in the region's border protection, saying it is stronger since the introduction of the PNG deal.
"We've got about 13 customs officers on the islands, as well as a team that can fly out from here at Cairns at short notice, a team of six," he said.
"On top of that we've got two helicopters at Horn Island, and we've got two boats at Thursday Island, so we've got the resources on the ground."
He said there were 10 illegal arrivals in the Torres Strait last year and 10 so far this year.
