The Immigration Department has agreed to pay compensation to Save The Children after some of its workers were removed from Nauru in 2014 amid allegations they were coaching asylum seekers to self-harm and inciting protests.

In a statement, the Department said it regretted its decision to remove the staff, and that payment of money was not adequate compensation.

It also acknowledged it did not provide Save the Children or the employees with detailed reasons for the removal.

"Although SCA (Save The Children) is no longer providing services for the Department on Nauru, the Department affirms SCA's good standing with it and acknowledges that at the time of the removal direction and subsequently, it had no reason to cause doubt to be cast on SCA's reputation," it said.

At the time of the removal, Save The Children management and staff were only made aware of the allegations by a front page newspaper article in the Daily Telegraph under the headline "Truth Overboard".

Two independent reports commissioned by the Federal Government dismissed the allegations and recommended the department offer compensation.

In initial negotiations with the workers, Save The Children's lawyers said they were hoping for a figure of just under $1 million for loss of income and consolation for pain and suffering, hurt and humiliation and damage to reputation.

This settlement is yet to be reached.

But the agreed figure with Save the Children has been settled confidentially.

Mat Tinkler, director of policy and public affairs at Save the Children, said the group welcomed the decision.

"It is a relief," he said. "This has been a very difficult chapter in our organisation and we're very pleased to reach agreement with the Department of Immigration and Border Protection today."

"We have been in touch with the workers to let them know this has happened. This was a very difficult and traumatic experience for the staff; they are all now pursing their own claims against the Government."

In a statement, Greens Senator Sarah Hanson-Young said the allegations were proven to be baseless.

"The shameful practice of the Government, which is to blame the victims and those advocating for them, has backfired," she said.

One of the workers, Poppy Browne, told 7.30 in February that the removal from Nauru still haunted her.

"For the last 10 years of my life I have dedicated my life to working in the child protection field, in the social work field, and to have my name associated with allegations as serious as that, it broke my heart," she said.