Last week, a San Francisco jury acquitted Zarate of murder and manslaughter in the 2015 shooting death of Steinle.
Prosecutors said Garcia Zarate deliberately fired into an unsuspecting crowd on the pier in July 2015, killing Steinle as she walked with her father.
Federal prosecutors Tuesday said new immigration and weapons charges have been filed against Jose Ines Garcia Zarate, an undocumented immigrant who was acquitted last week on murder charges in the fatal shooting of San Francisco resident Kate Steinle.
A federal grand jury on Tuesday handed down an indictment of Jose Ines Garcia Zarate for a pair of felony gun charges.
San Francisco District Attorney George Gascon on Tuesday defended his office's handling of the case.
Garcia Zarate, who is from Mexico and has been deported from the United States five times, faces up to 10 years in prison on each count, if convicted.
Garcia-Zarate's public defenders said the shooting was accidental, that the gun went off unintentionally after Garcia-Zarate found it wrapped in a rag beneath a bench.More news: Liverpool win Group E with Coutinho hat trick
Garcia Zarate had been deported five times before the 2015 shooting. He said he still believed Garcia Zarate should have been convicted of Steinle's murder.
The Justice Department indictment makes no mention of the state's murder or manslaughter charges of which Zarate was acquitted.
The case sparked a fierce debate over sanctuary cities, and forced San Francisco officials to defend its policy.
Under a sanctuary city law, San Francisco authorities released him from custody three months before the shooting, instead of turning him over to Immigration and Customs Enforcement.
Sanctuary City policies, which have been in place in San Francisco in some form since the 1980s and are used by several hundred other cities and counties nationwide, are meant to promote public safety by encouraging immigrants to report crimes and cooperate with police.
Trump in a tweet called the not guilty verdict in the case "disgraceful" and said "No wonder the people of our Country are so angry with Illegal Immigration".
However critics have argued they encourage crime, and the current administration has made several attempts to punish Sanctuary City jurisdictions by withholding federal grant funds.