Customs and Border Protection (CBP) Commissioner Kevin McAleenan told reporters in Texas the prosecution referrals were suspended last week.
He said it followed an order last week by President Donald Trump calling for an end to migrant family separations.
But Mr Trump had suggested the families would instead be detained together.
The Republican president bowed to public pressure last Wednesday, signing his executive order to "keep families together" in migrant detentions.
Mr McAleenan maintained that the Trump administration's "zero tolerance" tactics were still in effect, although the commissioner's guidance to his agents largely leaves the policy in limbo.