Echuca CFA captain Rob Amos said it was still unknown what caused the fire, which was reported about 6.20pm.
"It's a fuel fire so it's going to take a while to cool down," he said.
The man driving the boat, who is believed to be from out of town, suffered burns to his feet and the back of his head and was taken by ambulance to Echuca hospital.
"He seems okay but he's pretty lucky," Mr Amos said.
Echuca's Trevor and Katrina Mottram were in their own boat when they heard the explosion..
"I heard na na na na boof," Trevor said.
"He was heading out and first start, it went up.
"I could feel the heat coming off it."
Katrina said she saw the man, believed to be in his 50s, scrambling to get out of the boat.
"He's so lucky," she said.
"I grabbed the fire extinguisher and started running over there but he pushed me away."
"He was pretty shaken up," Trevor said.
"His feet got the worst of it."
Trevor said this served as a reminder for boat owners to check their vessels before starting them.
"I've heard that sound enough times," he said.
"It shouldn't happen. It's just maintenance. People should be checking their boats and lifting the covers."
The boat fire in Moama started after the vessel had been refuelled, causing vapours to accumulate.
However, Mr Amos said he didn't know if the same thing had happened with this boat.
"I'm not sure about the age of the boat, I don't think it's that old," he said.
"However, what people need to know if that if you're going out in a boat and you haven't been out for a while, fumes may have accumulated under the bonnet, particularly on a hot day like today and if the fumes are forced out of the motor, that can cause it to ignite it gets hot," he said.
Two CFA tankers attended the fire, as well as Echuca police and Ambulance Victoria.
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