Early figures from the Australian Electoral Commission show about 5.65 per cent of votes nationwide would not count because they were filled out incorrectly on Saturday or left blank.

The high number of informal votes has been dubbed "The Mark Latham Effect" after the former Labor leader urged people to throw their vote away.

Only 3.95 per cent of votes were informal at the 2007 election.

In the Hunter, 5385 informal ballots had been cast in Charlton, 7.11 per cent of the total.

In Shortland 5023 informal votes made up 6.58 per cent of the total votes.

Re-elected Shortland MP Jill Hall said her scrutineers reported a large number of people who appeared to have mistakenly voted informally.

"They said there was a really high proportion of people who voted '1' and didn't number the other boxes," Ms Hall said.

The only Hunter seat that recorded below-average informal votes was the marginal contest at Paterson, where 4049 votes were not counted.

Australian Electoral Commission spokesman Phil Diak said they would examine why there were so many informal votes.

"Blank votes for the 2007 election were a very small number, below 1 per cent of the overall vote. I guess we'll have to take a look at all the ballot papers this time," Mr Diak said.