The Jetstar spokesman said it wasn't uncommon for planes to be struck by lightning when flying through bad weather.
He said aircraft were designed to safely withstand lightning strikes.
It was earlier reported Sydney's desalination plant was damaged and three people were injured after a tornado tore through the city's south with winds of more than 200km/h.
Sydney Airport was closely monitoring the storm activity with passengers being advised to check flight details with their airlines, an airport spokeswoman said.
There would be some delays and diversions, Sydney Airport tweeted.