Liberal Democrat Tim Quilty and Derryn Hinch's Justice Party MP Tania Maxwell both spoke against the initial 12-month extension on Tuesday, but were not persuaded by the government's agreement to reduce the extension to six months.

The debate lasted until 2am Wednesday morning, before the move was eventually passed 20 votes to 19.

It will be debated by the lower house today, but is expected to pass because Labor has a majority in that house.

Mr Quilty says he was "deeply disappointed" the government was granted an extension of emergency powers.

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He turned his displeasure to Samantha Ratnam from the Greens, Fiona Patten of the Reason Party and Andy Meddick of the Animal Justice Party, who voted with the government.

"They have allowed civil liberties to continue to be trampled by a government which is so incompetent that it has had to extend its emergency powers to tidy up its own mess," he said.

"My office received many thousands of emails expressing disgust at this legislation and urging me to vote against it.

"These same people will not only be as disappointed as I am, they will also be furious at the implications."

Mr Quilty said one email sent to his office stated: "Mummy, I'm really sad, I feel so lonely in my head and feel like I have no one, we can't even go anywhere or see friends or Nanny and Pa, I'm just so sad".