Parts of the airport have also been partially flooded after the roof of Terminal 1 leaked due to the heavy rainfall.
Much of Victoria was under a thunderstorm warning this afternoon, including Maryborough, Ballarat, Melbourne, Traralgon, Sale and Moe.
The Bureau of Meteorology said the storms were likely to produce heavy rainfall that may lead to flash flooding, damaging winds and large hailstones in the warning area over the next several hours.
A Melbourne Airport spokesperson said the storm had resulted in a number of “significant water leaks” across multiple terminals.
“We are currently cleaning up the impacted areas,” the spokesperson said.
“The safety of passengers and staff is our top priority. Now that the storm has passed, ground staff have resumed operations and are working to safely get passengers to their destinations.”
The spokesperson said all aerodrome operations, which include staff working on the airside, were temporarily suspended due to the risk of lightning strikes.
“This has resulted in delays to a number of inbound and outbound flights,” the spokesperson said.
“We apologise to passengers for the inconvenience.”