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Opposition leader Steven Marshall says it is too early to call the result of South Australia's Fisher by-election, but admits the count has so far been disappointing for the Liberals.

The counting of votes is continuing on Monday with Labor's Nat Cook ahead of Liberal Heidi Harris 51.4 per cent to 48.6 per cent on a two-party preferred basis.

The Liberals had been expected to win the seat, but Mr Marshall said on Monday the party always knew it was going to be a "complex by-election".

He said the party faced an anxious wait while the pre-poll and postal votes were counted, and the results may not be known for days.

Premier Jay Weatherill said the swing to Labor showed voter dissatisfaction with broken federal coalition promises as well as with the "pathetically weak" reaction to them from the SA opposition.

Senior Liberals admitted Defence Minister David Johnston's insult about not trusting SA-based shipbuilder ASC "to build a canoe" played a large part.

Federal MP Andrew Southcott said national issues played a part in the votes, while Assistant Infrastructure Minister Jamie Briggs said the canoe comment was "very, very unhelpful".

"People, I think rightly, expect us to be empathetic and that comment was not that," he said.

Bob Such, who won Fisher from Labor in 1989, served as a Liberal MP for 10 years before becoming an independent in 2000.

He was diagnosed with a brain tumour a week after the 2014 state election and died in October.

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Tense wait for SA Libs in by-election