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(CNN) —  

Health and Human Services Secretary Alex Azar now estimates that under 3,000 kids who may have been separated from their parents are in government custody – a figure far higher than his department released just nine days ago.

HHS had previously reported that it had 2,047 children from separated families in its care.

During a call with reporters, Azar did not provide an exact number of children separated from families, but said that “a review and comprehensive audit of multiple data sets” undertaken by HHS and the Department of Homeland Security indicated that fewer than 3,000 total children, including an estimated 100 under the age of 5, are in the care of Office of Refugee Resettlement-funded grantees. The HHS secretary said that number refers to children “who may have been separated from their purported parents who were taken into DHS custody for having crossed illegally or for other reasons like concerns for the safety of the child.”

President Donald Trump reversed course last month and signed an executive order intended to keep families together, but the administration is still facing scrutiny and questions over the families separated as a result of its widely-criticized “zero-tolerance” immigration policy.

The administration is now also grappling with a series of court-imposed deadlines after a judge ordered the US government to halt most family separations at the border and the reunification of separated families.

Azar said on Thursday that HHS “will comply with the artificial deadlines created by the court,” but that federal officials are focusing for now on confirming family matches prior to reunification.

“We will use every minute of time that we have to confirm the parentage of those individuals who are asserting that they are the parents of these children,” he said. “Then we will comply with the court’s order and reunify them. … We have not sent children into ICE custody yet, pursuant to the court’s order, but we will do so as we approach the court’s deadline.”

Azar attempted to clarify why HHS is now estimating a figure of under 3,000 children by saying that the department is working under the constraint of the court order.

“Because of the court’s order, we are starting from the largest potential data set that we have. We don’t want to be under-inclusive. We’re airing on the side of inclusion,” he said. The court order, Azar said, “goes back indefinitely. It’s not about ‘zero-tolerance’ … so it’s a much broader and inclusive set than any number that we would have discussed with you before, hence the larger number.”

Azar also confirmed on Thursday that the government is conducting DNA testing as part of its family reunification effort. “We are also doing DNA testing to confirm parentage, quickly and accurately,” he said.

CNN’s Catherine Shoichet, Sonia Moghe, Sunlen Serfaty and Laura Jarrett contributed to this report.