A first flight of migrants landed Tuesday in Guatemala with a second due Thursday, the ministry announced in a statement.
Foreign ministry spokeswoman Patricia Letona said the flights would contain groups of around 50 people including children and that two more were scheduled for next week.
Though flights with unaccompanied minors from the U.S. have continued, general deportations by air to Guatemala were suspended in mid-May.
The flights have caused tensions between the U.S. and Guatemala because dozens of people sent back to the Latin American nation tested positive for coronavirus. At least 186 deportees have tested positive for COVID-19 after arriving in the country despite the U.S. assuring they were in good health.
Guatemala’s government said deportees would be screened for the virus and that only its citizens held in U.S. Immigration and Customs Enforcement (ICE) detention centers were coming back.
“The decision (to restart flights) was made on the basis of technical sanitary information,” Letona said.
The Foreign Ministry says about 5,500 Guatemalans are in the custody of the ICE. More than 2,500 of those have a final deportation order and the remainder still have a pending process.
The administration of U.S. President Donald Trump has pressured Guatemala to keep receiving deported migrants despite widespread concerns returnees are bringing coronavirus with them and could infect remote communities.
News of the resumption was met with resistance from migrant advocacy groups inside Guatemala.
Director of Casa del Migrante migrant shelter and priest, Mauro Verzeletti, said Washington’s decision was “major mistake” and would not help conditions in Guatemala.
“This is only going to cause more racism against the returnees in their own country,” he told Reuters. “We’re still closed and we’ll re-open once the curve of the pandemic has come down.”
Since the epidemic began in Guatemala in mid-March, the country has received 2,160 deportees from the U.S.