The chances of Clive Palmer’s PUP Party winning a third Senate seat have been thrown into doubt.

The Australian Electoral Commission says it is checking if hundreds of ballot papers for the West Australian Senate were mistakenly placed in the informal pile during counting.

PUP candidate Zhenya Dio Wang appeared to have won the seat by 14 votes but there were appeals for a recount.

The Electoral Commission initially decided against a recount but changed its decision after an appeal by the Greens Senator Scott Ludlam.

The Australian Electoral Commission’s Phil Diak says about 400 votes have been identified as possibly having been counted incorrectly as informal.

Those votes have been referred for central Senate scrutiny.

Mr Diak says the outcome of the re-count should be known by the weekend.

“This is just part of a re-count where you do look again at all the informal votes,” he said.

“It’s just that with the below the line votes, we know that there were 62 boxes below the line in Western Australia, it’s more complex.

“We have a computerised process that helps us check whether the vote is formal or not.”

Mr Diak says they have recounted 700,000 of the 1.2 million votes so far.

“We’re working through it as quickly as we can,” he said.

“We’re over half way through the re-count but it’s some hundreds of thousands of votes to go yet, so we don’t have a definitely forecast of when we will complete.

“But we are working through it as quickly as we can and we hope it’s not too far away.”