Question: I have a worker who has moved from a 417 Visa to a 482 Visa in Sep 2019.
He was also exempt from medicare until the 13 Jan 2020.
However it appears as the medicare levy is being assessed against both the income while under 417 and 482 

Answer: According to ATO Medicare levy is 2% of taxable income. And both 417 and 482 incomes are included in the taxable income. Hence medicare levy should be presented. Ref: https://www.ato.gov.au/Individuals/Medicare-and-private-health-insurance/Medicare-levy/