The comprehensive reform will also see fee adjustments for other services, such as hospital stays and consultations at specialist and family medicine outpatient clinics.
But the administration is also introducing an annual cap of HK$10,000 for each patient, while pledging to make it easier for eligible people to apply for a fee waiver.
Health minister Lo Chung-mau said the fee reform was meant to offer more help for the underprivileged and those with severe illnesses.
He stressed that the extra revenue will go back into public healthcare.
Under the proposal, public A&E departments will charge patients depending on their condition, instead of the current flat rate of HK$180.
Critical and emergency cases will be treated for free, while the rest will have to pay HK$400 per visit.
The authorities are also introducing a “co-payment model” to charge patients between HK$50 and HK$500 for advanced and highly complicated pathology and non-urgent imaging tests.
Basic check-ups with high demand will remain free.
Fees for medicine from specialist and family medicine outpatient clinics will also be adjusted, while patients will be prescribed no more than four weeks’ worth of drugs each time.
The changes are expected to lower the government’s subsidy ratio for public hospital services from 97.6 percent to about 90 percent, which officials said remains a high level.
At the same time, the government will relax the income and asset requirements to qualify for a fee waiver. About 1.4 million people are expected to benefit after the tweak, up from 300,000.
The HK$10,000 annual fee cap, meanwhile, is estimated to help about 70,000 chronic or severely-ill patients who visit hospitals frequently.
Officials aimed to complete the fee reform within five years, and conduct reviews every six months.