The result of the Fisher by-election in South Australia remains too close to call.

The Liberal Party had been expected to win the seat, but Labor has polled strongly and leads on a two-party preferred basis.

It could be days until the result is known with about 7,000 postal votes to be counted on Tuesday.

About 24 per cent of people cast postal and pre-poll votes, which are likely to determine the result.

The Liberals need more than half of the postal and pre-poll votes to win the seat.

Opposition Leader Steven Marshall said it was going to be an anxious wait until postal and pre-poll votes were counted.

"This was always going to be a complicated by-election," Mr Marshall said.

"Our early polling showed that it was marginal, it was complicated and it just goes to show [that] nothing is for certain in politics."

Voters unhappy with Coalition Government: Weatherill

Labor candidate Nat Cook casts her vote in the seat of Fisher. ( ABC News: Candice Marcus )

Premier Jay Weatherill claimed the early results were a message to the Federal Government that voters were unhappy.

Mr Weatherill suggested concern over the future of submarines in South Australia was a factor.

"This was an issue that was very much on the minds of the voters of Fisher," Mr Weatherill said.

"It was something that was regularly mentioned to us when we door-knocked and spoke to people on the phone.

"I think both the Victorian result and now this Fisher by-election result sends the clearest possible message to the Federal Liberal Government that they should keep their promise to build submarines here in Australia."

Mr Woodyatt was endorsed by Lyn Such, the wife of the late Bob Such who had held the seat since 1989.

He said he was relatively happy with the result.

"We would like to have been a one or two per cent difference at this stage," Mr Woodyatt said.

"There was a stage where we were sitting before when Reynella got announced when it was 22 to 23.

"That was strong, that was a winning position, so we've retracted a bit from that and will come down to a close count of the remaining votes."

Adelaide University political commentator, Dr Clem McIntyre, said there would be recriminations within the Liberal party, even if it wins the Fisher by-election.

Dr McIntyre said dissatisfaction with federal Coalition policies played a part in the way people voted.

He said even if the Liberal candidate Heidi Harris won, it was a bad result for the Liberal party.

"They've had a huge fright here, even if they just snatch victory on the flow of preferences," Dr McIntyre said.

"I think there's some real concerns for the Liberals about why they've not been able to convince people in a seat like Fisher, which we think of as a traditional Liberal seat, that they pose an alternative government."

Complaints about how-to-vote cards

Earlier in the day Mr Woodyatt complained to the Electoral Commission about how-to-vote cards by Rob De Jonge.

"This election could come down to a few hundred votes and Rob De Jonge had put a card out that had put those votes through to the Liberal Party and that was not what he declared to the electoral commissioner," he said.

Mr De Jonge's how-to-vote cards were not the same as he gave to the Commission.

"I'm allowed to change my mind surely in the middle of an election, sometimes things happen," he said.

Dr Bob Such, a former Liberal minister before becoming an independent, held the seat until he died in October from a brain tumour.

He first won the seat of Fisher in Adelaide's south in 1989 and become an independent in 2000.

Other candidates contesting the seat are Greens candidate Malwina Wyra, Independent Australian Democrats' Jeannie Walker, Stop Population Growth's Bob Couch and independents Dan Woodyatt, Dan Golding and Rob de Jonge.