By Dominic Giannini in Canberra

Illegal fishing vessels entering Australian waters are being destroyed in an effort to protect marine life from poaching.

Dozens of Indonesian fishing boats have been set alight by Australian Border Force patrols in recent weeks, Operation Sovereign Borders Commander Rear Admiral Brett Sonter says.

More than 200 boats were seized, 48 sunk and 1000 fishermen apprehended in two operations in Australia’s north, he told Seven News.

Border Force has teamed up with the Indonesian navy to tackle the problem.

Cabinet minister Jason Clare warned against the practice.

“Illegal fishing is a serious thing. Anyone coming into our backyard and stealing things out of your backyard is serious,” he told Seven’s Sunrise program on Friday.

“The only way to stop it is to burn their boats, send a message that if you do this, you will lose the most valuable thing you have got, your boat.”

Deputy Liberal Leader Sussan Ley backed the operations.

“As a former environment minister, I’m very concerned about illegal fishing,” she said.

Ms Ley also raised concerns about the boats being used by people smugglers.