The fire, which police believe is not suspicious, started while the boat was on the water at Lake Nagambie at around 3.20pm on Sunday, February 8.
Advanced Life Support and Mobile Intensive Care Ambulance paramedics responded to the scene.
An Ambulance Victoria spokesperson said two female children were taken by road ambulance to Goulburn Valley Health in a stable condition.
“Fortunately, no-one was seriously injured,” a Victoria Police spokesperson said.
The investigation into the incident is ongoing.
Anyone who witnessed the incident or with further information is asked to contact Crime Stoppers on 1800 333 000 or report at crimestoppersvic.com.au
Man dies at Lake Eildon
A man has died at Lake Eildon at the weekend.
Emergency services were called to an area near Jerusalem Track at about 2.30pm on Sunday, February 8.
Two men had reportedly entered the water, but could no longer be seen.
One man was found and given CPR on the shore before being taken to hospital in a serious condition.
The second man, aged 22, from Cairnlea, was located shortly after, but was unable to be revived.
Investigations are ongoing.
Man dies at Lake Nillahcootie
Police will prepare a report for the coroner after a man died at Barjarg, south of Benalla, at the weekend.
Emergency services were called to Lake Nillahcootie at about 1.45pm on Saturday, February 7, following reports the man had been pulled unresponsive out of the water.
CPR was performed on the 21-year-old, from Dandenong, but he was unable to be revived.