It was unclear whether the FBI explicitly ordered the digital attacks, but court documents and interviews suggest "that the government may have used hackers to gather intelligence overseas," the Times wrote.
The figure at the center of the case is Hector Xavier Monsegur, who had become a prominent hacker with the activist group Anonymous, which has staged cyber assaults on MasterCard, PayPal and other commercial and government targets.
Monsegur was arrested by the Federal Bureau of Investigation and became an informant, helping the law enforcement agency identify other members of Anonymous.
Monsegur instructed a fellow hacker, Jeremy Hammond, to extract data from a long list of foreign government websites. And then that information -- which included bank records and login details -- was uploaded to a server "monitored" by the FBI, the Times reported, citing court papers.
The vast target list for hacking added up to more than 2,000 Internet domains, including the Polish Embassy in Britain and the electricity ministry in Iraq, according to an uncensored court document cited by the Times.
Monsegur and Hammond had previously worked together to sabotage servers for Strafor Global Intelligence, an intelligence consultant firm based in Austin, Texas.
"After Stratfor, it was pretty much out of control in terms of targets we had access to," Hammond told the Times in an interview from a federal prison in Kentucky, where he is serving a 10-year sentence for the Stratfor attack and other hacking.
Hammond said he and Monsegur learned of a vulnerablity that could be exploited in web-hosting software called Plesk, which permitted backdoor access to thousands of websites.
A court sentencing statement said that Monsegur directed other hackers to pull data from Syrian government sites, including banks and various ministries, according to the Times.
"The FBI took advantage of hackers who wanted to help support the Syrian people against the Assad regime, who instead unwittingly provided the US government access to Syrian systems, said the court statement quoted by the Times.
Monsegur's location is unknown and his sentencing hearing has been delayed repeatedly, fueling speculation that he remains an informant for the US government, the Times wrote.
The report reinforces allegations that the US government has exploited flaws in Internet security to spy on foreign targets.
The FBI was not immediately available for comment.
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Pakistan government should sue FBI in international court of justice as this act is against the sovereignty of our country and violates UN international law
Pakistan Army seriously needs a Cyber Command which can work with civilians to secure the nation's electronic networks. This sort of activity is only going to get worse. Also, I'm very surprised that there is no debate on the 13.5 billion intercepts NSA makes in Pakistan, second only to Iran, or the 100,000 bugged devices that NSA has sent out since 2008. Palantir detected an espionage network within the Indian Defense Ministry, you think something similar doesn't exists in Pakistan?