Trump administration is "trying to make citizens afraid of immigrants and make immigrants afraid of law enforcement," critics say.
There have been reports that DHS does not routinely consult social media during the vetting process for visa applications.
The news comes a week after an internal TSA investigation found major holes in security at America's busiest airports.
The President's executive action on immigration, which includes deportation relief for millions of illegal immigrants, will remain in place.
An estimated 85 percent of DHS workers will still report to work, though without pay.
Obama's immigration policies in dispute.
His ruling means the Homeland Security department may not shut down—for a while.
If called up, the National Guard will provide humanitarian assistance in the region, which has been badly hit by the Ebola outbreak.