Mr Azar told reporters in a call on Thursday that the Department of Health and Human Services (HHS) would use the "faster" method of testing in order to meet a court order to reunite children aged four and under by 10 July and children aged five to 17 by 26 July.
HHS had previously reported that it had 2,047 children from separated families in its care.
The DNA verification has been expedited to comply with the court's timeline, although the government worries that some cases could prove to be more complex and might not be verified by the imposed deadline.
And how many kids from separated immigrant families are still in government custody? Azar had said Thursday that "under 3,000" children had been separated from their parents.
USA officials are now rushing to reunite more than 2,000 children separated from their parents at the border after the court in San Diego ordered the government last month to halt the practice.
U.S. officials have resorted to DNA testing on up to 3,000 detained children who remain separated from their migrant parents, a top official said Thursday as President Donald Trump's administration struggles to rapidly reunite families at the center of a border crisis. The process was being carried out "as expeditiously as possible", he said.
He said the new number reflected a more thorough look by HHS at its case files, and over a longer time period, to comply with the court order that families be reunited.
'At the same time, however, the Government has a strong interest in ensuring that any release of a child from Government custody occurs in a manner that ensures the safety of that child'.
Jennifer Falcon from the immigration advocacy group Raices tweeted earlier that the decision was "further proof the administration has no idea how to reunite families".
HHS has always been charged with caring for unaccompanied minors crossing the border, thousands of children every year.
"To comply with the Ms. L injunction, the government will not separate families but detain families together during the pendency of immigration proceedings when they are apprehended at or between ports of entry and therefore subject to the Ms. L injunction", the DOJ lawyers wrote an older document attached to the new filing.
U.S. District Judge Dana Sabraw in San Diego has ordered the youngest children reunited by Tuesday of next week, and the rest before the end this month.
Even as the Trump administration implemented its zero tolerance crackdown on immigration - which saw immigrant children split up from their parents and transferred to specifically designated shelters and foster care systems run by the Office of Refugee Resettlement - reports emerged that the government was ill-equipped to undo the logistical nightmare it had set into motion. A court hearing on the administration's efforts and plans is scheduled for tomorrow.
Azar's agency, Health and Human Services, supervises migrant detention centres. Administration officials said it was a temporary measure only to free up space in processing centers. "Tell the people "OUT", and they must leave, just as they would if they were standing on your front lawn".
Attorney General Jeff Sessions, who oversees immigration courts, has narrowed the parameters for those seeking asylum, arguing that domestic violence or gang violence is not grounds to grant it - a blow to people arriving from Central American countries like El Salvador that have been ravaged by violent street gangs.