The Trump administration is using DNA testing to reunite up to 3,000 migrant children separated from their families by the government’s “zero tolerance” immigration policy, but claims it may miss a court-imposed deadline to do so.

Alex Azar, secretary of health and human services, said of the children in his department’s care, about 100 were aged under five.

Last month, as the president issued an executive order to halt the separation of families, federal judge Dana Sabraw ordered that children under five years old be reunited with their parents by July 10, and for all children to be reunited by 26 July. He also ordered that parents have phone contact with their children by Friday 6 July. Officials are due to provide an update on what progress has been made.

Mr Azar told reporters on Thursday his department would “comply with the artificial deadlines created by the court”.

“HHS (Health and Human Services) knows the identity and location of every minor in the care of our grantees. And HHS is executing on our mission, even with the constraints handed down by the courts,” he said.

However, Reuters reported that overnight, the government asked a federal court for further guidance on how to reunite parents and children before the deadline expires. A filing by Department of Justice officials to the District Court for the Southern District of California, said in some cases, the government may need additional time.

The government, in its filing overnight, said the process could further be delayed by steps that were required before parents could be reconnected with their children, according to its interpretation of the court order, the news agency said. This included DNA testing to verify parentage, a criminal history check, and assurance that parents could provide for the child’s physical and mental well being.

Melania Trump visits Arizona border patrol facility: 'I'm here to support you'

“HHS anticipates, however, in some instances it will not be able to complete the additional processes within the timelines the court prescribed, particularly with regard to class members who are already not in government custody,” they wrote.

Jonathan White, an HHS official said in usual cases, documents were used to identify people, with DNA providing a backup when paperwork was not available. The deadlines set by the court now means officials were using DNA as a primary means to identification.

“Because of the compressed timeframe, the typical process of using documentation is not going to be completed within the timeframe allowed in this case by the court decision for the great majority of these children,” he said. “And for this reason the decision has been made to use a faster process of DNA verification to confirm that biological relationship.”

Undocumented immigration across the US-Mexico border Show all 14 1 /14 Undocumented immigration across the US-Mexico border Undocumented immigration across the US-Mexico border Immigrant children, many of whom are separated form their parents, are housed in Texas' tent city Reuters Undocumented immigration across the US-Mexico border A two-year-old Honduran asylum seeker cries as her mother is searched and detained near the US-Mexico border Getty Undocumented immigration across the US-Mexico border Undocumented migrants ride on the top of a freight train referred to as the beast, or La Bestia Getty Undocumented immigration across the US-Mexico border A cage inside a US Customs and Border Protection detention facility in Texas Reuters Undocumented immigration across the US-Mexico border US Border Patrol Academy All new agents must complete a months-long training course at the New Mexico facility before assuming their posts at Border Patrol stations, mostly along the US-Mexico border Getty Undocumented immigration across the US-Mexico border US-Mexico border fence A group of young men walk along the Mexican side of the US-Mexico border fence in a remote area of the Sonoran Desert Getty Undocumented immigration across the US-Mexico border US-Mexico border fence in the US Man looks through US-Mexico border fence into the US in Tijuana, Mexico Getty Undocumented immigration across the US-Mexico border US-Mexico border fence US Border Patrol agent Sal De Leon stands near a section of the US-Mexico border fence while stopping on patrol on in La Joya, Texas Getty Undocumented immigration across the US-Mexico border US Border Patrol Academy US Border Patrol instructor yells at trainees after their initial arrival to the academy Getty Undocumented immigration across the US-Mexico border Memorial service in Guatemala Families attend a memorial service for two boys who were kidnapped and killed in San Juan Sacatepequez, Guatemala. Crime drives emigration from Guatemala to the United States, as families seek refuge from the danger Getty Undocumented immigration across the US-Mexico border Arrests on the border Undocumented immigrants comfort each other after being caught by Border Patrol agents near the US-Mexico border Getty Undocumented immigration across the US-Mexico border Detention holding facility A boy from Honduras watches a movie at a detention facility run by the US Border Patrol Getty Undocumented immigration across the US-Mexico border Mexican farm workers Mexican migrant workers harvest organic parsley at Grant Family Farms in Wellington, Colorado Getty Undocumented immigration across the US-Mexico border Mexican family in Arizona A Mexican immigrant family sits in the living room of their rented home in Tuscon, Arizona. The family that Arizona's new tough immigrant law had created a climate of fear in the immigrant community. Getty

Mr Trump triggered international outcry last month when it emerged more than 3,000 children had been separated from their families after immigration officials adopted a new policy to charge every migrant apprehended trying to enter the nation illegally.

The children are typically not sent to adult detention facilities, meaning thousands of families were broken up – something which was widely condemned by campaigners and high-profile figures – including the first lady. The policy has also resulted in large protests in many cities across the US.

A number of charities and activist groups are helping in efforts to reunite families and provide legal services.

The South Texas Pro Bono Asylum Representation Project, a programme established by the American Bar Association, has been providing legal help to immigrants and asylum-seekers, particularly unaccompanied children.

The government’s ‘zero tolerance’ immigration policy drew widespread condemnation across the US (EPA)

“In the current crisis, the staff are providing legal services to detained children and coordinating groups of volunteer Spanish-speaking lawyers, who have come from throughout the country to provide legal services to adults,” said spokesman, Matthew Cimento.

The children separated from their families were dispatched to private facilities located across the country, contracted by the federal government to look after the youngsters, the youngest of which was just nine-months.

Hundreds of children were sent to New York City and upstate New York, without the knowledge of Governor Andrew Cuomo or New York City mayor Bill de Blasio – both of whom have criticised the Trump administration’s actions.

On Friday, an official in the mayor’s office, who asked not to be identified, told The Independent the mayor’s goal was “for all the separated kids to be reunited with their families and loved ones”. He said officials were in touch with staff from the federal government on how to help with reunification.

“We have seen a tremendous outpouring of support for separated families from New Yorkers, with people seeking ways to help. The mayor’s fund is collecting monetary donations for organisations and legal service providers helping these kids,” the official said.