The government’s new system that grants citizenship has “alarming” security breaches, including allowing immigrants to be approved without a full FBI background check, the Homeland Security inspector general said Monday in an “urgent” warning telling officials to put everything on hold.

Inspector General John Roth said he got wind that U.S. Citizenship and Immigration Services was about to take the troubled system online later this month, and said he was compelled to issue the extraordinary alert to try to prevent a massive mistake.

He said that as of Jan. 11, about 175 citizenship applications were approved despite never having completed the background checks.

“Without sufficient vetting, immigrants could potentially be granted U.S. citizenship although they are ineligible or pose national security threats,” Mr. Roth said in his alert.

He first made his appeal to USCIS on Jan. 19, the day before the change in administrations. He released his public “urgent” appeal at noon Monday.

Mr. Roth said after the agency was alerted to the 175 applications it had wrongly approved, it started to redo them.

Dubbed ELIS, or the Electronic Immigration System, the new process was deployed last April and quickly ran into problems.

The inspector general said it failed to make “core” checks it was required to make, kept canceling applicants’ appointments and ruined the workflow, forcing officers to end up processing applications manually anyway.

The entire system was halted last year as the problems became clear.

Mr. Roth said USCIS was prematurely rushing to get it back up and running this month.

He’d planned to issue a full report later in the year, but said USCIS’ move forced him to issue his immediate warning.

“Although we are only in the beginning phases of our review, we have already identified significant operational and security issues that pose grave concern,” Mr. Roth said.

USCIS didn’t respond to a request for comment on the new warning, but last year the agency acknowledged it was aware of problems when it suspended the electronic system.

An internal email obtained by House Judiciary Committee Chairman Bob Goodlatte last year showed how deep the concerns ran.

“At this point we are not confident that proper FBI Name Checks have been run on certain ELIS cases. At this point we are uncertain of the scope of the problem,” Daniel M. Renaud, USCIS associate director, said in an email.

Mr. Goodlatte demanded answers on when USCIS learned of the problem and how many cases it affected.

He said the agency should move to strip citizenship from anyone who was wrongly approved.

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