The agreement, brokered by rebel supporter Qatar and regime ally Iran, is expected to involve more than 30,000 people, the Syrian Observatory for Human Rights said.
The deal reached late yesterday involves Zabadani and Madaya, besieged by regime fighters near Damascus, and Shiite-majority Fuaa and Kafraya in northwest Syria that are encircled by rebels.
Such evacuations have been touted by President Bashar al-Assad as a way to end his country's six-year war, but his opponents say the regime is redrawing Syria's map with forced displacement.
In the central city of Homs, where evacuations from the last rebel-held district resumed last month, a bomb struck a bus today, killing five people, state media said.
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The Observatory, a British-based monitor of the war, said the residents of Zabadani, Madaya, Fuaa, and Kafraya are to quit their hometowns over the course of 60 days starting next week.
All of the residents of Fuaa and Kafraya are expected to leave, while it was unclear if the evacuations of Madaya and Zabadani would empty the towns completely.
"The evacuations are not expected to begin until April 4 but, as a goodwill measure, a ceasefire for the towns came into effect overnight," Observatory chief Rami Abdel Rahman.
"It is calm there now," he said, adding that the truce would last nine months.
Islamist rebels in the northwest province of Idlib have signed on to the deal, under which 32,000 people are expected to be evacuated, Abdel Raman told AFP.
At least 600,000 people are living under siege in Syria, according to the United Nations, with another four million people in so-called "hard-to-reach" areas.
They last received humanitarian aid deliveries in November.
The UN, which oversaw the initial agreement, has admitted that the "tit-for-tat arrangement" has complicated efforts to get aid in.
The UN's humanitarian office in Damascus told AFP today that it "was not part of the agreement or the negotiations."
The Syrian Arab Red Crescent, meanwhile, confirmed that it would take part in evacuations but could give no further details.
The regime has been accused by rights groups of the torture and summary executions of thousands of people in its prisons and intelligence services headquarters.
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