The surprise defeat of Sri Lanka's longest serving leader should force Australia to review its immigration policies and "unprincipled and problematic relationship" with the country, human rights advocates say.

On Friday, the leadership of Mahinda Rajapaksa was overthrown by his former health minister Maithripala Sirisena who made the shock decision to run against Rajapaksa in the election just six weeks ago.

Until now, Australia's increasingly cosy relationship with Rajapaksa, who was in his 10th year of power, has been heavily criticised by human rights groups under both the Labor and Coalition governments.

In November 2013 the Abbott government gifted the country two boats to help stem the flow of asylum seekers and then refused to back an independent international investigation into the country's alleged war crimes in February.

"As part of its one-eyed obsession with stopping the boats, the Australian government has ignored, condoned and even abetted human rights abuses in Sri Lanka," said Emily Howie, Director of advocacy and research at the Human Rights Law Centre.