A bill to remove all children from onshore immigration detention centres has passed the Senate with the support of the Greens, Labor and crossbenchers.

Amendments put forward by Greens senator Sarah Hanson-Young also call for greater media access to detention centres, with refusals to be tabled by the Immigration Minister Peter Dutton.

The amendments passed the upper house with the support of Labor, as well as crossbenchers Ricky Muir, David Leyonhjelm, Nick Xenophon, Dio Wang and John Madigan.

The amended Migration and Maritime Powers Amendment Bill (No.1) will now return to the House of Representatives, where it is likely to be sunk by the government majority.

Senator Hanson-Young said she hadn't spoken to Prime Minister Malcolm Turnbull about the amendments today, but was confident that "Modern Malcolm" would be uncomfortable voting them down.

"I suspect this is an issue for Malcolm Turnbull to decide," she said.

"He either has to vote now to re-detain children, to lock journalists out of detention centre and to gag staff, or he sees the sense... I can't imagine Malcolm Turnbull feeling very comfortable about voting in the house to re-detain kids."

The Greens had initially proposed five amendments, though one calling for the "separation of people seeking asylum from criminals in immigration detention" was voted down.

Other adopted amendments related to the mandatory reporting of abuse witnessed within detention centres, as well as the reversal of secrecy provisions detailed under Section 42 of the Border Force Act.

Prolonged detention detrimental to children: Welfare agency

Welfare agency Save the Children has called on the Turnbull Government to support the amended bill, and extend it, to cover children in offshore immigration detention centres.

The group had previously provided education and welfare to detainees — including children — on Nauru prior to their removal last month.

In a statement, Save the Children spokesman Matt Tinkler said the amendment limiting the detention of children to 30 days should be extended.

"Our experience working with asylum seekers and refugees on Nauru and Manus Island before that tells us that detaining children for prolonged periods is detrimental to their mental and physical wellbeing," he said.

"We urge the Turnbull Government to bring on the legislation for debate, and pass the amendments as a matter of urgency."