Scott Morrison says he was doing the job he had to do as immigration minister when the federal government wrongly claimed aid workers were coaching asylum seekers to self harm.
Save the Children has now been compensated and received an apology from the immigration department on Friday over the matter.
In 2014 the immigration department directed the group to remove 10 of its staff from the Nauru regional processing centre.
Nine were then deported by the Nauru government and one had already left.
The department was acting on allegations the staff had orchestrated protests, coached and encouraged self-harm of detainees, criticised the regional processing system and leaked confidential information.
Two subsequent independent reviews found the information available to the department at the time did not warrant directing the workers be removed.
Mr Morrison, now the treasurer, said on Sunday he was pleased the matter had been concluded.
"This has been a very difficult issue over a long period of time," he told ABC TV.
But he stopped short of apologising himself to Save the Children.
"Those evidences that were presented to me, I had investigated fully by a proper process. I did the job I had to do in that situation," he said.
