"Our readers are understandably interested to know about guns in their neighborhoods," Royle said in her statement.
In an article about the uproar, The Journal News says many of the thousands of people who "have taken to their computers and phones in rage" live outside the counties covered by the map.
In searching through hundreds of comments listed on the website, CNN did not immediately see any in support of the newspaper's decision to publish the interactive map.
The Journal News said it published an article in 2006 that received similar responses, but this time around, social media spread the story far and wide.
In 2007, roanoke.com, the website of The Roanoke Times, published a list of Virginians licensed to carry concealed weapons, and then deleted it the next day. The paper explained that the list, originally published as part of an opinion column, was removed "out of concern that it might include names that should not have been made public."
The Poynter Institute, a school for journalists, notes that some other news agencies have published various types of databases as well.
"Publishing gun owners' names makes them targets for theft or public ridicule. It is journalistic arrogance to abuse public record privilege, just as it is to air 911 calls for no reason or to publish the home addresses of police or judges without cause," Al Tompkins, a Poynter senior faculty member, said in a statement Wednesday. "Unwarranted publishing of the names of permitted owners just encourages gun owners to skip the permitting."
The paper said Royle was not available for interviews Wednesday.