Every echo of this story leads back to the same original source:
Rick Ellis, a Minneapolis-based journalist for Examiner.com, reports that these cities also had the help of the Department of Homeland Security and the Federal Bureau of Investigation.
Calling Ellis a journalist is really talking about his past, as Examiner.com is not a journalistic operation. It is a glorified bloghost that hands out locality and topical concessions to whoever wants them. If you'd like to be the Fargo correspondent on the topic of alien abductions, head on over and sign up... Ellis' claimed source for federal involvement is a single anonymous DoJ employee. No serious journalistic operation would publish a story on such a thin thread, particularly given the on-the-record denials of federal involvement. Veterans of Usenet will recognize his claim as akin to the classic "the lurkers support me in email" assertion.
Beyond that weakness, it is helpful to understand the background of Examiner.com. It is a property of Clarity Media, which also owns dead-tree newspapers using the Examiner name in SF, DC, and Baltimore and The Weekly Standard. A sibling company owns The Oklahoman. A watcher of media would note the common thread here: strident right-wing publications unconcerned with issues of fact or journalistic integrity. The whole bunch is owned by Philip Anschutz, who is something of a native-born Rupert Murdoch, except that he avoids media coverage himself and is more of a partisan theocrat than a pure devotee of money. Anschutz has bankrolled a menagerie of anti-gay, anti-porn, and anti-science entities such as Colorado for Family Values, Discovery Institute, Media Research Council, Institute for American Values, and so on. He also is the main backer of the Narnia films and has helped prop them up via his Regal Entertainment Group theater chain. In short, Anschutz is someone with a history of spending large amounts of money on evangelism, propaganda, and disinformation in support of a far-right Christian Dominionist agenda. Examiner.com is less purely bullshit than some other parts of Anschutz's media operations, but the rightward tilt is pretty clear behind the amateurism.
Even if Ellis isn't shilling for Anschutz and has a real source at DoJ, it is also important to recognize the failed status of the DoJ. Under Ashcroft and Gonzales, there was a project of political hiring for staff positions that mutated in 2008 into 'burrowing' of Bush appointees into civil service slots. Since 2009, GOP Senators have used their 'hold' privileges to prevent many appointments in DoJ (and elsewhere) so there are a lot of empty chairs at DoJ and some Bush holdovers to go along with the "Loyal Bushie" staff and the burrowing. In short: there is an ethically problematic population of anti-Obama partisans at DoJ, one of whom could be Ellis' anonymous source.
There is an interest on the Right in feeding the basic distrust of Obama in the Occupy movement. That distrust is not entirely baseless, but the legitimate issues (e.g. the courting of financial sector contributors, heavily compromised policies, etc.) aren't overwhelming. Convincing the Occupiers and their sympathizers that there is an active role being played by the Obama Administration in trying to collapse their movement serves the purposes of the GOP and of those to its right such as Anschutz. It should be expected by anyone watching politics that there will be a barrage of efforts to convince the Left that the Democrats who are actually electable to office are as unsalvageably corrupt and enslaved to Big Money as any Republicans. Some of that will be spinning of facts, some will be disinformation. This story smells strongly of disinformation.