Maltese residents entering the country without a vaccine certificate must apply for permission to avoid paying €1,400 to quarantine in a hotel.
The Superintendent of Public Health will decide each case "on an individual basis", the government said in a statement on Thursday.
It confirmed that people arriving from the 71 countries on Malta's 'red list' can enter without a vaccine certificate but they must provide a negative PCR test taken no more than 72 hours before their arrival.
They must then undergo 14 days of quarantine in a hotel at a cost of €100 per night, per room, "which will include breakfast", the statement says.
There is ony one approved quarantine hotel, the Marina Hotel in St George's Bay, which is close to capacity.
There are exceptions for unvaccinated children aged 12-15 who may undergo their mandatory quarantine at their permanent residence in Malta.
However, anyone living in the same household, even if vaccinated, must also quarantine for the same period of time.
Maltese residents over the age of 16 must apply for "authorisation from the Superintendent of Public Health to complete their quarantine period in an alternative residence."
The email address to use is: covid19.vetting@gov.mt
Those who cannot take the vaccine for approved medical reasons or are aged 11 and under do not have to undergo mandatory quarantine.
There has been mass confusion over the change in travel rules, with airlines denying people entry to Malta without vaccine certificates on Wednesday.
The guidance also confirms that Malta will accept vaccine certificates from Dubai and Turkey, as long as they show that the person has been fully vaccinated for at least 14 days.
Three other vaccine certificates are accepted: the NHS COVID Pass, the Maltese vaccination certificate and the EU COVID certificate.
However, this list of accepted certificates will be "updated from time to time".
The full 'red list' of countries is:
Austria; Cyprus; Czech Republic; Denmark; Estonia; Finland; Hungary; Iceland;
Ireland; Germany; Latvia; Lithuania; Luxembourg; Norway; Italy; France; Slovakia; Switzerland; Greece; Croatia; Spain; Poland; Belgium; Bulgaria; Netherlands; Canada; Australia; New Zealand; South Korea; Andorra; Monaco; San Marino; China; Vatican City; Israel; Singapore; Slovenia; Japan; United States of America but only limited to the following states Washington, Oregon, Louisiana, West Virginia, North Dakota, Georgia, Texas, Pennsylvania, North Carolina, Tennessee, Iowa, Nebraska, Ohio, South Carolina, New Mexico, Florida, Virginia, Maine, South Dakota, Michigan, Illinois, Delaware, Wisconsin, Puerto Rico, Hawaii, New Jersey, Minnesota, Connecticut, Alaska, New Hampshire, Maryland, New York, Rhode Island, District of Columbia, Massachusetts, Vermont, California, Idaho, Kentucky, American Samoa,
Federated States of Micronesia, Northern Mariana Islands, Palau, Republic of Marshall Islands, Arkansas, Missouri, Oklahoma, Mississippi, Virgin Islands, Nevada, Arizona, Wyoming, Utah, Alabama, Colorado, Guam, Indiana, Montana and Kansas; Gibraltar; Portugal; Romania; Lebanon; United Arab Emirates; Turkey; Jordan; Liechtenstein; Sweden; Belarus; Belize; Bosnia and Herzegovina; Bhutan; Fiji; Jamaica; Georgia; Faroe Islands; Kosovo; Kazakhstan;
North Macedonia; Montenegro; Moldova; Vietnam; Egypt; Iran; Libya; Panama; Qatar; Cuba;Serbia; Albania;Armenia; Azerbaijan; Saudi Arabia; the United Kingdom; Ukraine.
All other countries are on the 'dark red list', from where travel is banned.