Prime Minister Scott Morrison says he has cried “on his knees” over the plight of young asylum seekers held in Australian offshore processing centres on Nauru, in his most sympathetic public remarks on the issue to date.

Speaking at a lunch organised by suicide prevention service Lifeline, Mr Morrison said he had prayed for the children still on Nauru, confirming there were still just over 30 on the Pacific island.

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He said border security was a “moral burden” and said the issues were not “easy”.

“You'll find yourself on your knees, you'll find yourself in tears," he said.

Mr Morrison, a former immigration minister who helped engineer the Abbott government’s policy of boat turn-backs under Operation Sovereign Borders, said he believed asylum seeker advocates were well-meaning.

“I can understand that people who have a very different view to mine are motivated by the purest of motives. All I ask is that they might give the same benefit of the doubt to those with whom they might disagree with.”

READ MORE Less than 30 children left on Nauru, say advocates

The government has been quietly fling the children of asylum seekers and refugees held on Nauru to Australia for medical treatment, but insists they will not be allowed to settle in the country permanently.

They will either be returned to Nauru or settled in the United States.

Labor also supports offshore processing and the policy of never allowing those who come to Australia by boat to ever settle in the country.