Two of the groups are also asking the FCC to fine Comcast $195,000 for every affected subscriber.
The petitions will be the first real test of the FCC's stance on "Net Neutrality," the long-standing principle that Internet traffic be treated equally by carriers. The agency has a policy supporting the concept but its position hasn't been tested in a real-world case.
Last month, The Associated Press reported that Comcast hindered file sharing by subscribers who used BitTorrent, a popular file-sharing program. The AP's tests confirmed claims by users who also noticed interference with some file-sharing applications.
Comcast is the country's largest cable company and has 12.9 million Internet subscribers, making it the second-largest Internet service provider.
Comcast denies that it blocks file sharing, but acknowledged last week that it was "delaying" some of the traffic between computers that share files.
In practice, the company blocks requests from users who are trying to retrieve files from a Comcast subscriber's computer for a period of time. But it eventually lets the requests through if they are repeated.
In one AP test, a request went through after 10 minutes of trying. The technology does not directly affect downloads of BitTorrent files by Comcast subscribers, only uploads.
Comcast has said the interference is intended to improve the Internet experience for all its subscribers, noting that a relatively small number of file sharers is enough to slow down its network.
In response to the filings, David Cohen, an executive vice president at Comcast, said that the FCC's policies recognize that ISPs need to manage the traffic on their networks.
But if other ISPs follow in Comcast's footsteps, file sharing would essentially crawl to a halt. While the technology is a popular way to illegally share copyright movies and music, legal uses are proliferating, particularly in movie distribution.
"They're blocking an innovative application that could be a competitor to cable TV," said Marvin Ammori, general counsel at Free Press, one of the advocacy groups behind the petition to the FCC.
The petition asks the commission to immediately declare that Comcast is violating the FCC's policy. The co-signers are Consumer Federation of America; Consumers Union, the publisher of Consumer Reports; Media Access Project; Public Knowledge; and professors at the Internet practices of the Yale, Harvard and Stanford law schools.
Free Press and Public Knowledge are separately filing a formal complaint that asks the FCC to demand a "forfeiture" from Comcast of $195,000 per affected subscriber.
The number is based on the statutory maximum of $97,500 for a single continuing violation, doubled by what the groups see as deception on the company's part. Comcast kept its practice secret until publicized by the AP, saying that it couldn't divulge the inner workings of its network for security reasons.
Its filtering technique also involves the company forging network messages so that they appear to come from subscriber and non-subscriber computers.
The complaint includes affidavits from three Comcast subscribers who say they have been affected by Comcast's interference. The complaint asks the FCC to determine the total number of affected subscribers.
It's not clear how quickly the FCC would act on the filings.
"The FCC should be aggressively reviewing these cases because they go to ensuring the freedom and openness of the Internet which is so vital to our communications future and to our civic dialogue," FCC Commissioner Michael Copps said in a statement.
Comcast's Cohen noted that the FCC's policy statement, which says that consumers are allowed to run the Internet applications of their choice, makes that "subject to reasonable network management" by ISPs.
"If Comcast is right - that what it's doing meets the policy statement - then anyone can start blocking BitTorrent tomorrow," Ammori said.
A ruling against Comcast could cause problems for other Internet service providers. Many of them acknowledge managing traffic to improve flow, which likely includes slowing down file-sharing traffic by means less drastic than Comcast's.
The Net Neutrality debate erupted in 2005, when the FCC abolished the obligation of providers of Internet service via digital subscriber lines, or DSL, to carry all traffic nondiscriminately (that obligation had been abolished for cable broadband in 2002). The obligation was replaced with the policy statement.
Phone companies started suggesting that they would like to be able to charge large Web companies more for guaranteed delivery of their traffic as a way to finance the build-out of their networks.
Web anchors like Google Inc. and Amazon Inc., joined by consumer groups, opposed the notion, saying it would make Internet service providers the toll keepers of the Internet and enable them to stifle competition and innovation.
The debate was stilled when AT&T Inc. and Verizon Communications Inc. agreed to shelve their plans temporarily to get their respective plans to acquire BellSouth and MCI approved by the FCC.
Ammori said it appeared that the "nightmare scenario" portrayed by Net Neutrality proponents like his own group, Free Press, had been averted.
"Then suddenly, out of nowhere, Comcast is doing exactly what we most feared ... secretly degrading an application," Ammori said. "We didn't expect the first violation to be so blatant."