An independent news Web site says the Department of Justice ordered it to release detailed information on its readers -- then directed the site to keep quiet about the demand.

Kristina Clair, systems administrator for Indymedia.us, said she was shocked when she received a subpoena from U.S. Attorney Tim Morrison in Indianapolis in January demanding the IP address of every person who visited the site on June 25, 2008. She said she was also instructed "not to disclose the existence of this request unless authorized by the Assistant U.S. Attorney."

Clair said she was astonished by the demand. "It's a purely aggregate site, it only pulls data from other Indymedia feeds," she told FoxNews.com. "There's no information fed to the site directly."

When she contacted the Electronic Frontier Foundation (EFF), a legal advocacy group for digital freedom, she was told the subpoena was riddled with problems.

"Not only was this request a plain violation of federal privacy law -- which would require the government to at least get a court order based on a factual showing to get that kind of data; not only did it violate Department of Justice regulations that require subpoenas to media organizations to be vetted by the attorney general; not only did it threaten the First Amendment right to read anonymously of all of Indymedia's users, it also violated Ms. Clair's First Amendment rights by ordering her not to disclose the subpoena's existence," EFF Senior Staff Attorney Kevin Bankston told FoxNews.com.

EFF said it sent a letter to Assistant U.S. Attorney Doris L. Pryor on Feb. 13 relaying its concerns with the subpoena and explaining that Indymedia didn't store IP addresses and didn't have the data the government was looking for.

"On February 24, I received a voicemail from Ms. Pryor in response to my letter," Bankston said. "In that message, Ms. Pryor said that I was correct that the subpoena did not compel Ms. Clair's silence, but that she would be seeking a court order, as she would confirm in a letter later that day."

Instead, Bankston said, he received a fax from Pryor the next day stating that the subpoena had been withdrawn.

When he called the U.S. Attorney's office later that day to discuss the newly dismissed subpoena, Bankston said Steven DeBrota, the assistant U.S. attorney working on the case, told him the office had reconsidered seeking a court order for Clair's silence but still insisted that disclosure of the subpoena would harm the investigation.

Still, Bankston said, DeBrota would not confirm that Clair would face no legal consequences if she disclosed the subpoena, so EFF sent another e-mail asking for confirmation that there was no legal bar to disclosing the subpoena. Three months later, there was still no response, he said.

"So we wrote them again saying, 'If you actually think this is going to hurt your investigation, go to court and we'll fight it out there, otherwise we're going assume it's not going to hurt your investigation and we're going to speak out about it,'" Bankston said.

With no response to the May letter, EFF and Clair said they decided to go public with the subpoena and EFF's report critiquing it out of fear that this may not be an isolated incident.

"We don't know how many people have received these subpoenas -- that would violate the privacy of anyone that ever read their Web site -- but didn't say anything about it and didn't contact a lawyer because there was a gag order attached to it," EFF spokeswoman Rebecca Jeschke told FoxNews.com.

When asked about the EFF report, U.S. Attorney Morrison told FoxNews.com "we can't comment about that."

Morrison then directed FoxNews.com to Justice Department spokeswoman Melissa Schwartz, who said, "The U.S. Attorney's Office of Indiana South issued the subpoena and it's a grand jury investigation. They're [Morrison's office] the one's giving comment. ... Unfortunately, we [the Justice Department] can't comment on grand jury deliberations."

A source with knowledge of the situation said the subpoena in question required the signature of the attorney general -- or, in his absence, of acting Attorney General Mark Filip -- but that Filip's office never saw it, and the subpoena was never kicked up for approval.

The source would not say whether an internal investigation into the matter, specifically Morrison's actions, had been opened.