"Hacktivist" collective Anonymous took credit for taking down the sites Thursday after the arrests of leaders of Megaupload.com and shut down the popular hub for illegal media downloads.
Hours after the announcement of the arrests, some of Megaupload's fans turned the table on the feds, knocking the U.S. Department of Justice and the FBI websites offline.
Both sites appeared to be back up early Friday. A law enforcement official told CNN the FBI was investigating.
Anonymous said 10 websites in all were targeted and early Friday the sites for music publishing and licensing group, BMI and record company Universal Music were still down.
"The Site is under maintenance. Please expect it to be back shortly," was the message on the Universal Music page early Friday.
The hacker collective announced its attentions on Thursday.
"We Anonymous are launching our largest attack ever on government and music industry sites. Lulz," the group said in a statement posted late Thursday on an associated Twitter account. "The FBI didn't think they would get away with this did they? They should have expected us."
The group also posted personal information on former Connecticut Sen. Chris Dodd, chairman of the Motion Picture Association of America, one of the targeted sites.
A Justice Department spokesperson, who did not want to be identified, said its Web server was "experiencing a significant increase in activity, resulting in a degradation in service."
"The department is working to ensure the website is available while we investigate the origins of this activity, which is being treated as a malicious act until we can fully identify the root cause of the disruption," the spokesperson said.
The website glitches came soon after various Twitter accounts associated with the collective took aim at the government.
Anonymous' favorite weapon for these attacks is what's called a "distributed denial of service" (DDoS) attack, which directs a flood of traffic to a website and temporarily crashes it by overwhelming its servers. It doesn't actually involve any hacking or security breaches.
"One thing is certain: EXPECT US! #Megaupload" read one tweet from AnonOps that went out midafternoon.
One hour later, the same account tweeted a victory message: "Tango down! http://universalmusic.com & http://www.justice.gov// #Megaupload"
Speaking of the Web attacks, an Anonymous representative said 5,635 people used a networking tool called a "low orbit ion cannon." A LOIC is a software tool that aims a massive flood of traffic at a targeted site.
The news comes as lawmakers have turned their attention to anti-piracy legislation. Protests erupted both online and offline this week against two bills under consideration in Congress: the House's Stop Online Piracy Act (SOPA) and the Senate's Protect IP Act (PIPA).
The bills are aimed at cracking down on copyright infringement by restricting access to sites that host or facilitate the trading of pirated content. But the legislation has created a divide between tech giants, who say the language is too broad, and large media companies, who say they are losing millions each year to rampant online piracy. (Time Warner, the parent company of CNN, is among the industry supporters of the legislation.)
On Twitter, YourAnonNews said Thursday's attacks meant an "involuntary blackout" for sites of SOPA supporters.
Universal Music's website went down Thursday afternoon. The music company had been locked in a legal battle with Megaupload over a YouTube video that featured many of Universal Music's signed artists promoting Megaupload's site.
The websites of the Recording Industry Association of America and Motion Picture Association of America were out of action Thursday afternoon, but they appeared to be back up later in the evening.
A spokesman for RIAA cast the attack as a minor hiccup.
"The fact that a couple of sites might have been taken down is really ancillary to the significant news today that the Justice Department brought down one of the world's most notorious file-sharing hubs," he said.
The Anonymous attack came soon after the Justice Department announced the indictment of seven individuals connected to Megaupload for allegedly operating an "international organized criminal enterprise responsible for massive worldwide online piracy of copyrighted works."
Authorities said the operation had generated more than $175 million in illegal profits through advertising revenue and the sale of premium memberships.
According to the indictment, Megaupload, which launched in 2005, was once the 13th-most visited website on the Internet, serving as a hub for distribution of copyrighted television shows, images, computer software and video games.
The site's popular MegaVideo subsidiary was widely known in tech circles for its copious selection of pirated content, including recent movies and episodes of hit TV shows.
Four of those indicted were arrested Thursday in Auckland, New Zealand, at the request of the United States. Three others remain at large.
The individuals indicted are citizens of New Zealand, Germany, Slovakia and the Netherlands. No U.S. citizens were named. However, Megaupload has servers in Ashburn, Virginia, and Washington, which prompted the Virginia-based investigation.
To shut down Megaupload, federal authorities executed 20 search warrants in eight countries, seizing 18 domain names and $50 million worth of assets, including servers in Virginia, Washington, the Netherlands and Canada.
In some of its attacks, Anonymous has targeted governments or companies it says are part of or support a police state.
The list of police officers and agencies targeted by the collective is long. From New York to Oakland, California, police websites have been hacked; personal information, including the home addresses of specific police officers, was posted online in 2011.