Special Minister of State Michael Ronaldson announced on Friday that Mr Killesteyn had formally tendered his resignation to the Governor-General.

The High Court this week declared last September's West Australia Senate result void - paving the way for a fresh election in the state - after more than 1300 ballot papers went missing during the counting process.

Mr Killesteyn is on personal leave and will remain so until his resignation takes effect on July 4.

Deputy electoral commissioner Tom Rogers will act as commissioner.

''Events in Western Australia mean that the Australian Electoral Commission must regain the confidence of the community,'' Senator Ronaldson said.

Palmer United Party leader Clive Palmer, who has been a fierce critic of the commission for losing the ballot papers, said Mr Killesteyn had done the right thing by resigning.

He felt sympathy for Mr Killesteyn but it was important that he be held accountable.

Last year, Mr Killesteyn apologised unreservedly for the lost ballots.

On Friday, Labor spokesman Gary Gray said it was his understanding that Mr Killesteyn had always intended to leave his role before the next federal election, due in 2016.

''Ed Killesteyn is an outstanding public servant. His service over past decades has been of the highest calibre,'' he said. ''The last months have been a difficult time, and Mr Killesteyn handled them with great integrity.''

Mr Killesteyn was appointed in January 2009 and last year Labor extended his term for another five years.