The former Daily Show host was testifying before the judiciary committee's subcommittee about securing more money to help care for members of the emergency services who became ill after responding to the attacks.
But most of the panel's 14 members failed to show up.
"Sick and dying, they brought themselves down here to speak and no one," Stewart said.
"Shameful, it's an embarrassment to the country and a stain on this institution. You should be ashamed of yourselves for those who aren't here but you won't be because accountability doesn't appear to be something that occurs in this chamber."
Becoming tearful, he continued: "Where are they? It would be one thing if their callous indifference and rank hypocrisy was benign, but it's not.
"Their indifference cost these men and women their most valuable commodity, time, the one thing they're running out of."
Retired NYPD bomb squad detective, Luis Alvarez, was part of the attack response team.
He told the hearing: "Less than 24 hours from now, I will be serving my 69th round of chemotherapy... I should not be here with you. But you made me come. You made me come because I will not stand by and watch as my friends with cancer from 9/11 like me are valued less than anyone else."
Other emergency service members sat behind Mr Alvarez wiping away tears.
He continued: "We were there with one mission and we left after completing that mission. I have been to many places in this world and done many things. But I can tell you that I did not want to be anywhere else than Ground Zero when I was there.
"I have been lucky enough to have had 68 rounds of chemo. You heard me right. 68 rounds. Many others haven't had the opportunity to have five. Some have had none.
"It is my goal and it is my legacy to see that you do the right thing for all 9/11 responders.
"You all said you would never forget - well I'm here to make sure that you don't."
The fund, originally approved for five years in 2010, provides medical treatment for those who require ongoing care due to inhaling toxic dust in the days following the attack.
Republicans were unhappy with the cost of the original legislation and as a compromise at the time, Democrats agreed to authorise the fund for five years and cover the cost with an excise tax, with a re-evaluation every five years.
Stewart criticised congress for continuing to require the fund be renewed every five years - pointing to the panel's top Republican, Mike Johnson, for saying that congress has to balance other emergencies as well.
"I'm pretty sure what's going to happen five years from now, more of these men and women are going to get sick and they are going to die and I am awfully tired of hearing that it's a 9/11 New York issue," Stewart said, adding: "Al Qaeda didn't shout death to Tribeca."
More than 40,000 people have applied to the Victim Compensation Fund, which covers illnesses potentially related to being at the World Trade Center site, the Pentagon or Shanksville, Pennsylvania, after the attacks.
More than $5bn in benefits have been awarded out of the $7.4bn fund, with about 21,000 claims pending.
Stewart criticised the fact that nearly 18 years after the attacks, first responders and their families still have no assurance the fund will not run out of money.