Labor's Anne Aly has claimed victory in the Perth-based seat of Cowan, becoming the first Muslim woman elected to the House of Representatives.

Dr Aly, an anti-terrorism and de-radicalisation expert, also believed the Liberal campaign to paint her as soft on terrorism backfired and did not lose her any votes.

Incumbent Liberal MP Luke Simpkins has not conceded defeat, with the Liberal Party stating several thousand votes remained to be counted and it would wait to see how they fell.

But WA Labor says it has won the marginal West Australian seat.

The declaration came after the Australian Electoral Commission confirmed it had mistakenly placed about 200 Greens votes in Mr Simpkins' pile in the northern booth of Tapping.

After preferences were allocated, Dr Aly received 160 of the votes pushing her lead against Mr Simpkins out to 787.

Labor calculated there was no way he could now close the gap, even though almost 10,000 mostly absentee votes remain to be tallied.

'Diverse parliament in trying times a positive'

Dr Aly said she was humbled and looked forward to becoming a strong and fair voice in parliament for the Cowan community.

She said she recognised the significance of becoming the first Muslim woman in the Lower House of federal parliament.

"I think having a diverse parliament in these very trying times is an absolute positive and bodes well for the future of Australia," Dr Aly told reporters.

During the campaign, Liberal frontbenchers criticised Dr Aly's judgement, claiming she had provided support to radical Islamic preacher Junaid Thorne during his trial for flying with a false identity.

She countered it was a smear campaign and the de-radicalisation program she had suggested for Thorne was funded by the Coalition government.

Dr Aly said she did not think the criticism had played a huge role in the Cowan result.

"I do believe it backfired, whether or not it actually helped, I think that's a long short to call, that's a difficult call to make," she said.

"But I do believe it did backfire. But it certainly didn't lose me any votes."

Mr Simpkins, who has held the seat since 2007, declined to comment.