"If people want to be political activists, that's their choice, but they don't get to do it on the taxpayer's dollar and working in a sensitive place like Nauru," Morrison said.
"Making false claims and worse allegedly coaching self-harm and using children in protests is also completely unacceptable, whatever their political views or whatever their agendas."
Morrison said 10 workers from the Save the Children charity were to be removed from the small Pacific island.
"I should stress these removals do not relate to any suspected misconduct regarding sexual abuse or misconduct," he said.
Save the Children, which provides services to children on Nauru, denied that its staff had fabricated abuse stories or encouraged asylum-seekers to self-harm.
"Children have taken the drastic step of sewing their lips together and refusing food and water in protest at their indefinite incarceration in the Australian government's detention centre on Nauru," spokesman Ian Woolverton said.
"Our staff have responded to these distressing incidents with professionalism and compassion."
Australia's offshore processing of asylum-seekers has faced criticism from the United Nations and rights groups over conditions in the camps and the lengthy process of assessing their claims.
Morrison has previously said his party's asylum-seeker policies were effective in stopping people from dying at sea by deterring them from boarding boats bound for Australia.
The minister said he expected the independent investigation to have an interim report within seven weeks, with a final report by the end of the year.
Limited time offer:
Just RM5 per month.
