In Västra Götaland, Småland, and Blekinge as much as 40 milimetres of rain is expected overnight into Saturday.
In addition, the agency has warned of a high risk forest fires in northeastern Östergötland and along Sweden's northeastern coast.
On Thursday night, a series of heavy thunderstorms caused power outages, fires and serious flooding in many parts of Sweden.
Worst hit was the Götaland region in the west of the country.
The storms not only caused power outages, but also triggered a number of alarm systems, causing chaos throughout the region.
Jönköping County in central Sweden was also hard hit.
A bolt of lightning struck the Polkagris pre-school near Gränna causing a small fire. Staff on site were able to extinguish the fire however before the authorities arrived.
Meanwhile much of nearby Huskvarna was plunged into darkness when the electricity went down, and small fires were reported in several areas.
The town of Nässjö also suffered widespread flooding. In one area outside the town there were reports of a flood almost 100 metres long and as deep as one metre in some areas.
A cold front will be moving north across Sweden in the next few days bringing with it the threat of flash fires in several regions, most notably in the north of the country, according to SMHI.