The UAE on Wednesday barred entry to travellers from Zambia, the Democratic Republic of Congo and Uganda.
The measures include national and overseas airlines as well as transit passengers arriving on them.
Transit flights travelling through the UAE and those destined for the above countries are exempt from the ruling.
The ruling will come into effect from 11.59pm on Friday.
On Monday, Uganda's president Yoweri Museveni introduced new lockdown measures to tackle a wave of Covid-19 cases among young people.
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Coronavirus third wave - in pictures
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He announced the closure of schools and universities for 42 days and suspended public gatherings and prayers in mosques and churches.
On June 4, the country recorded 1,259 cases, the highest in a single day, with officials reporting long lines at hospitals. President Museveni saying the wave mostly affected people aged between 20 and 39 – and an increase in transmission rates among children aged 10 to 19.
Last week, the Democratic Republic of Congo said it was facing a third wave of coronavirus infections, with its epicentre in the capital, Kinshasa, one of Africa's most populous cities.
Health Minister Jean-Jacques Mbungani said the country was in the middle of a third wave and cited a low vaccination rate and poor observance of hygiene practices for the rising infection rate.
The UAE decision was announced by the National Emergency Crisis and Disaster Management Authority and the General Civil Aviation Authority on on Wednesday.
The directive includes travellers who were in the three countries in the 14 days before coming to the UAE.
UAE citizens and first-degree relatives, diplomatic missions approved between the Emirates and the three countries, including administrators working in the embassies of the UAE and the affected countries, are exempt from the ban.
The exemptions include official delegations and businessmen, provided they obtain prior approval, as well as holders of golden and silver residency visas.
Those working in sectors deemed vital by the Federal Authority for Identity and Citizenship and crews of foreign freight and transit planes are also exempt from the ban on condition they present a negative Covid-19 test taken 48 hours prior to their departure.
Those excluded from the travel ban must adhere to precautionary measures, including undergoing 10-day quarantine, take a PCR examination at the airport and on days four and eight of entering the country.
"The General Authority of Civil Aviation confirmed that travellers coming from Zambia, the Democratic Republic of Congo and Uganda through other countries are required to have a period of stay in those countries of not less than 14 days in order to be allowed to enter the country, with the continuation of cargo flights between the UAE with the three countries," the crisis and disaster authority said.
"The authority called on all passengers affected by the decision to follow up and communicate with the airlines associated with them to modify and schedule their flights and ensure their safe return to their final destinations without any delay or other obligations."
