As part of the defamation settlement between the former attorney-general and the broadcaster, announced in June, they agreed to seek an order that 27 pages of the 37-page defence be permanently removed from the file.

But Nine and News Corp opposed the granting of such an order, arguing that usually when a case is settled, the documents remain on the Federal Court file and are available for inspection.

Justice Jayne Jagot previously made an interim suppression order on the 27 pages after Mr Porter raised an objection on the basis that they contained "scandalous" and "vexatious" material, or matters that were "otherwise an abuse of the process".

But his interlocutory application for parts of the defence to be struck out did not go ahead, as the parties agreed to settle.

Justice Jagot on Friday ordered that the unredacted defence be removed from the file, sealed in an envelope and stored elsewhere in the court records.

It is "not to be opened or made available for inspection by the public other than by leave of the Court".

The MP sued the ABC over a February 26 article about a now-deceased woman's claim he had raped her decades earlier. He denies the allegation.

The judge noted that parties could not expect a court to act as a "rubber stamp" approving whatever form of an order they agreed.

In this case, the deed specified they were to "seek" the removal order and its actual removal was not a condition of settlement.

"An important function of a court is also to facilitate the settlement of disputes by parties on terms agreed between the parties," she said.

"Provided the terms are lawful and the agreement does not affect the rights or interests of third parties, it would be rare for a court to refuse to give effect to a settlement agreed between the parties."

The ABC and journalist Louise Milligan had consented to the compromise reached, which included seeking the removal order.

The parties were not seeking "special treatment" as the court rules permitted such applications and for them to be granted, the judge said.

For the court to refuse to make the order would "be to undermine the lawful contractual bargain which the parties struck to compromise all of their claims".

She said the settlement meant parts of the ABC's defence would "remain allegations which will never be the subject of judicial determination".

The removal of the document was "necessary to prevent prejudice to the proper administration of justice", she concluded.

As part of the settlement, an editor's note was added to the article stating the ABC "did not intend to suggest that Mr Porter had committed the criminal offences alleged".

"The ABC did not contend that the serious accusations could be substantiated to the applicable legal standard - criminal or civil," it said.

"However, both parties accept that some readers misinterpreted the article as an accusation of guilt against Mr Porter. That reading, which was not intended by the ABC, is regretted."

Australian Associated Press