As the remnants of Cyclone Yasi are likely to strike northern South Australia (SA) over the weekend, emergency services on Thursday were preparing for rain and flash flooding in the area.

Queensland endured a night of terror as Cyclone Yasi, the category five storm, struck early on Thursday morning 1am (AEST), delivering 290km/h winds and raging seas. More than 170,000 properties are without power across north Queensland.

Prime Minister Julia Gillard said while the worst of Yasi appears to be over, some areas are expected to be hit by a second, dangerous storm surge on Thursday.

The weather bureau in SA said it is becoming clearer the remnants of Cyclone Yasi will have a big impact on northern areas of SA this weekend.

Vince Rowlands from the bureau said it would not be just be a typical summer storm.

"It is unusual to see once a cyclone does hit landfall to push so far inland with such a high intensity," he told ABC News on Thursday.

"The winds associated with this certainly lead to the possibility of some severe thunderstorms up there where we might be looking at much stronger wind gusts and heavier rainfall out of these storms."

According to State Emergency Service acting regional commander Bluey Devine, preparations had been made for any possible event in the remote areas.

"At this stage we are expecting more of a rain event rather than severe winds," Devine told Australia Associated Press on Thursday.

He said current forecasts estimate rainfall between five millimeters and 50mm, with possible heavy falls of up to 100mm. A flood watch has been issued for some areas in the state for Saturday and Sunday.

Meanwhile, South Australia on Wednesday experienced thunderstorms with winds over 50km/h, which has damaged houses and infrastructure in the Spencer Gulf and mid-north regions of South Australia.

Devine said trees fell on powerlines and some roofing iron and a granny flat were damaged.