The Turnbull government has paid an estimated $1 million in compensation and formally apologised to nine charity workers who were ejected from Nauru in 2014 after unsubstantiated claims of political activism and impropriety.

The Save the Children cohort was removed from the island under former immigration minister Scott Morrison, who cited an intelligence report accusing the group of encouraging asylum seekers to self-harm in order to be brought to Australia.

Subsequent reviews found that decision was "not justified" and was based on "no conclusive evidence", and called on the government to compensate the charity and its workers. Last week's settlement to individual former employees is in addition to the undisclosed sum paid last year to Save the Children itself.

In a statement, the Department of Immigration and Border Protection said it regretted the hurt, embarrassment and reputational damage its actions had caused the nine workers.