Some wineries reported more than 30 millimetres of rain and two-centimetre hailstones, which damaged local vineyards.
Katnook Estate winemaker Wayne Stehbens said the vintage started on the day of the downpour last week.
He says quality should not be affected but disease could become a problem.
"The conditions that we've got are conducive to disease, so there's an expectation that there will be some disease pressure as a result of this," he said.
"We're all fairly confident, we've got some hot weather and hot weather is normally really good to combat and high disease pressure so, touch wood, although we've had a bit of bad luck to start vintage this hot weather may work in our favour."