A 16-year-old Guatemalan boy has died in a Texas hospital after he was detained by Customs and Border Protection (CBP), becoming the third migrant child to die in US government custody in the past five months.

The boy, who has not been named, died on Tuesday at a Texas children’s hospital in the McAllen area after several days in intensive care. The cause of death has not been released.

It was unclear where and when the boy was detained, but on the evening of 20 April, he was taken by Immigration and Customs Enforcement (Ice) agents to a facility run by Southwest Key – a not-for-profit organization which houses up to 5,000 migrant children in more than 20 shelters – apparently in good health.

He was taken to an emergency room the following morning with symptoms including fever, chills and a headache, but discharged back to the shelter later that day.

The youngster’s health did not improve, according to a statement by Administration for Children and Families (ACF), and he was returned to the emergency room by ambulance on 22 April.

From there, the sick boy was admitted to an intensive care unit, where he died just over a week later.

The boy was under the care of the Office of Refugee Resettlement, which contracts private companies and registered charities to house thousands of children separated from their parents at the border by Ice officials – as well as those detained after making the perilous overland journey from Central America without adult relatives.

Two other children died in US custody within three weeks of each other in December 2018, but unlike in the latest case, they were in custody of CBP.

Jakelin Caal, seven, who died on 8 December at an El Paso children’s hospital, and Felipe Gómez Alonzo, eight, who died on Christmas Eve at a New Mexico hospital, were also Guatemalan – part of a mass exodus from the impoverished Central American country in recent months.

In November, Guatemalans overtook Mexicans as the largest nationality taken into CBP custody – an extraordinary figure considering that the population of Mexico is seven times larger than that of its southern neighbour.

Southwest Key has yet to comment on the child’s death, but ACF spokeswoman Evelyn Stauffer said in a statement: “Arrangements were made for the minor’s brother and Guatemalan consular officials to visit the minor while he was hospitalized. The family who resides in the home country received frequent updates from hospital staff. The cause of death is currently under review, and, in accordance with standard ORR policies and procedures, the case will be subject to full review.”

Southwest Key has collected $1.7bn in federal grants in the past decade, according to a New York Times investigation. Its founder resigned in March amid questions over its handling of government funds.

The Guatemalan consul in McAllen has been contacted for comment.