Cyber Command -- better known as CYBERCOM -- officially started attacking the tech-savvy IS group in April, in what was the command's most important offensive since being established in 2010.
Thomas Atkin, the acting assistant defense secretary for homeland defense and global security, said a "careful balance" needed to be struck, when asked why the military does not simply stop jihadists from accessing the Internet.
"It's a careful balance, even in Raqa or Mosul (in Iraq), or anywhere on how we balance the rights to have access to the Internet versus the use of the Internet illegally by folks like ISIL," Atkin told the House Armed Services Committee, using an IS acronym.
Officials said the IS group's online use was a source of valuable intelligence, but Republican committee chairman Mac Thornberry expressed concern Atkin was arguing Raqa citizens have "some sort of inherent right" to access the Internet.
The jihadists have used their social media savvy to deliver propaganda and disseminate their vision for a so-called caliphate across parts of the Middle East.
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Though Pentagon chief Ashton Carter has frequently touted CYBERCOM's offensive against the IS group, most details remain classified.
CYBERCOM deputy leader Lieutenant General Kevin McLaughlin said the Pentagon has gained important experience fighting the IS group online.
"It's given us the opportunity to learn and mature and kind of plow back in lessons learned in a real circumstance that it might have taken us several years to learn," McLaughlin told lawmakers.
According to the New York Times, CYBERCOM has placed "implants" in IS networks that let experts monitor the group's behavior and ultimately imitate or alter commanders' messages so they unwittingly direct fighters to areas likely to be hit by drone or plane strikes.
Another technique likely being employed is a common type of cyber attack known as a denial of service.
In a sign of the strategic importance virtual warfare now plays, lawmakers said it was time for CYBERCOM to stand up as its own combatant command -- an organizational super structure normally arranged along geographic boundaries.
CYBERCOM has about 4,700 troops, but is set to expand to 6,200 in 2018.