Guatemala City - Guatemala will temporarily stop receiving Hondurans and Salvadorans returned from the United States under the asylum cooperation agreement due to the coronavirus pandemic, Guatemala's foreign ministry said on Tuesday.

"As of today, all flights under [the Asylum Cooperation Agreement] are suspended," Foreign Minister Pedro Brolo said, referring to an agreement between Guatemala and the US.

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Guatemala will also stop receiving Guatemalans deported from the US until the Central American country and the US establish protocols to guarantee the health of migrants and asylum seekers before they are deported, officials said.

Tuesday's decision was made after meetings between Guatemala's Foreign Ministry, the ambassadors from the US, ambassadors from the region, and representatives from both state agencies and organisations from civil society that work with those deported from Mexico and the US.

The move came after President Alejandro Giammattei announced on Monday the suspension of all flights, a ban on all foreigners from entering the country and the closure of the country's borders for 15 days in an effort to stem the spread of the novel coronavirus.

The country had already banned the entry of citizens of European countries, Iran, China, North and South Korea, the US and Canada.

More than 900 Honduran and Salvadoran asylum seekers have been sent to Guatemala under the so-called "safe third country" agreement, which was signed in July 2019. The agreement allowed US immigration authorities to require asylum seekers who first cross through Guatemala to apply for asylum there instead of being eligible to apply in the US.

On Monday, one deportation flight chartered by the United States Immigration and Customs Enforcement (ICE) agency arrived in Guatemala. On board were 56 Guatemalans and 17 Salvadorans.

US officials did not immediately comment on the suspensions.

Migrant shelters close to deportees

In advance of Monday's announcement, the Catholic Church's Migrant Shelters in Guatemala City announced that it was temporarily suspending services to migrants and asylum seekers deported from the US and Mexico due to the growing crisis created by the pandemic.

"We cannot put at risk the lives of the people," Father Mauro Verzeletti, the director of the Guatemala City Migrant Shelter, told Al Jazeera.

The Migrant Shelter has given Hondurans and Salvadorans a place to stay and medical attention after being returned from the US as part of the asylum agreement.

"We are thankful at this moment there will not be the deportations of Hondurans and Salvadorans to Guatemala," said Father Juan Carbajal, the director of the Pastoral of Human Mobility, the national coordinator of migrant shelters in the country.

"We hope that this [suspension] will continue for a long time," he told Al Jazeera. "As we have said since the beginning, Guatemala does not have the conditions or preparation to receive these people. We hope they end these types of deportations."

More than 184,000 people have been infected with the novel coronavirus, according to the World Health Organization. More than 7,500 people have died. More than 80,000 people have recovered, according to John Hopkins University.

One person has died from the virus in Guatemala. President Giammattei announced on Monday that there were six active cases of coronavirus in the country. Another 300 people are under observation.