Labor's Nat Cook has been confirmed as the new member for the southern Adelaide seat of Fisher, taking out a recount of the by-election by just nine votes.

Ms Cook finished 23 votes ahead of Liberal candidate Heidi Harris in the first count, giving the South Australian Labor Government a majority in its own right.

The Electoral Commission approved the recount when the Liberals raised concerns about whether ballots marked with crosses as well as numbers should be considered as valid.

Liberal scrutineer Rob Lucas said while the result was disappointing for the party, the recount was justified.

"The margin has dropped to literally a fingernail polish difference, nine votes in the end, out of more than 20,000 votes," Mr Lucas said.

"Clearly there were a number of changes in formality of votes which were recorded through the scrutiny and the recount."

Labor scrutineer Michael Atkinson believed a challenge to the second count was unlikely.

"There are probably a couple of dozen of informal, potentially informal ballots that could go, have gone either way but I don't think a challenge to the recount could be launched on that basis because it ended up going fairly evenly," he said.

"We now have a final result that can withstand the most careful scrutiny."

Electoral Commissioner Kay Mousley yesterday said the re-count was approved to remove any doubt of a fair result.

"I think for transparency reasons it's best that we give a recount," she said.

"It is a close outcome and this way there can be no doubt in anyone's mind that we have got the right result."