The Trump administration has reunited just over half of the child migrants under the age of five who were forcibly separated from their families.

The Department of Health and Human services said on Thursday that 57 children had been "reunified" with their parents but they were not able to reunite the remaining 46 children.

Under President Donald Trump’s "zero tolerance" immigration policy more than 2,300 children were separated from their parents before he ended the system with an executive order last month.

Officials said the remaining 46 children were not eligible for "reunification" because some parents had already been deported, while others had been convicted of serious crimes, or were not in fact the parents of the children. 

It came after a California judge, Dana Sabraw, ordered the government to return the children to their parents by July 10.

Government officials argued they needed more time to carry out the task and provided an update on Thursday.

The government initially identified 102 children who fell into that category, and said 54 were now back with their parents. A further three have now been returned to their parents, officials announced on Thursday.

“As of this morning, the initial reunifications were completed. Throughout the reunification process our goal has been the well-being of the children and returning them to a safe environment,” the Health and Human Services Secretary Alex Azar, Homeland Security Secretary Kirstjen Nielsen and Attorney General Jeff Sessions said in a joint statement.

“Of course, there remains a tremendous amount of hard work and similar obstacles facing our teams in reuniting the remaining families. The Trump administration does not approach this mission lightly, and we intend to continue our good faith efforts to reunify families.”

The US Department of Justice also admitted that it might have mistakenly separated a toddler and father, who may be US citizens, for up to 12 months.

The "parent’s location has been unknown for more than a year," the department said.

The officials revealed that 12 adults had been deported and "are being contacted" and 11 are in US custody or jail for other offences.

They may be reunited with the children once they are located and contacted.

A further 22 children have not been reunited due to safety concerns which fall under "court-appointed criteria", the government said.  

These include a parent being treated for an infectious disease, 11 have a serious criminal history, while seven adults were "determined not to be a parent".

The Trump administration is also required to reunite children aged five and older – which includes around 2,000 – with their parents by July 26.

Judge Sabraw noted the government has "a lot of work to do" to reunite the older group and has ordered the Justice Department to provide an update Thursday.