Her wallet with a couple of hundred dollars cash and cards were also stolen.
"I was actually alerted by Westpac. I got a text message from them saying someone tried to spend $1000 online using my debit card of all things, not my credit card," she said.
"Within two hours of stealing the bag, they used the card by 6.29am at a local 7 Eleven three times to take out different amounts of money just using the pay pass."
Ms Cooke, who won her first Gold medal at 51, said the medals would be priceless to someone else.
"People can't actually sell them. Nobody will be able to sell them. I have a feeling they don't even realise they were in the backpack underneath all the clothes," she said.
Ms Cooke had the medals in her backpack ahead of filming with Monash University on Wednesday.
"As far as I'm concerned they are medals and I want to share them with people," she said.
"I take them to schools and everywhere that I talk and I pass them around. Especially with kids, I pass them around."
Ms Cooke was diagnosed with multiple sclerosis after competing in the Masters Swimming Nationals in 1998. She still lives with the never-ending symptoms of MS.
The Paralympian made an impassioned plea to return the medals.
"Just drop the backpack off, even in the Institute of Sport or a police station," she said.
