Agency officials apologized for the continued weaknesses and told a House subcommittee that they would do better. VA Secretary Eric Shinseki said he was taking disciplinary action.
The strong reaction came as the agency's inspector general reported that fewer than half of VA facilities selected for surprise inspections last month had proper training and guidelines in place. That was months after the VA launched a nationwide safety campaign over the discovery of errors at facilities in Georgia, Florida and Tennessee that could have exposed veterans to HIV and other infections.
John Daigh, VA's assistant inspector general who led the review, said the findings "troubled me greatly."
"We think there are systemic issues," Daigh said.
Lawmakers expressed disbelief that medical centers didn't immediately tighten procedures after the safety alert.
"You certainly would think that after the initial discoveries and the directive from the VA that medical directors would make sure that all of their equipment and procedures were brought into line and yet this investigation shows that many, many did not," said House Veterans Affairs Committee Chairman Bob Filner, D-Calif., who praised the VA for being transparent about the mistakes. "There will be a public accounting of this situation."
Army veteran Thomas Mayo got a colonoscopy after the VA insisted on it - only to learn it may have left him with a chronic disease.
"I'm really disappointed in them," Mayo told CBS News correspondent Nancy Cordes.
"Now I have to take the chance of losing my husband to this disease. And I don't want to lose my husband," said Mayo's wife Sandra.
In February, the VA began warning about 10,000 former patients in Georgia, Tennessee and Florida - some who had colonoscopies and other endoscopic procedures as far back as 2003 - that they may have been exposed to infections. They were advised to get blood tests for HIV and hepatitis.
The agency says that six veterans who took the follow-up blood checks tested positive for HIV, 34 tested positive for hepatitis C and 13 tested positive for hepatitis B. But there is no way to prove whether the infections came from VA procedures, and some experts say most or all of the infections probably already existed. The VA says the chance of infection was remote.
The VA has said - through self-reporting from all of its facilities - that such errors were limited to the centers in Murfreesboro, Tenn., Augusta, Ga., and Miami. But the inspector general report suggests problems could be more widespread because hospitals are using different equipment with varying degrees of training and standardized cleaning procedures.
CBS News medical correspondent Jonathan LaPook has performed thousands of colonoscopies.
"What stops contaminated fluids from backing up into this tube is this crucial green valve," he said, illustrating with a colonoscopy tube. "Investigators found not only was this valve missing, but this tubing wasn't being cleaned in between patients."
In surprise inspections at 42 VA medical centers on May 13 and 14, investigators found that only 43 percent had standard operating procedures in place and could show they properly trained their staffs for using their equipment.
VA officials struggled to explain the findings and said it would overhaul its procedures for colonoscopies and other common endoscopic procedures.
After the hearing, Shinseki issued a statement calling it "unacceptable that any of our veterans may have been exposed to harm as a result of an endoscopic procedure."
Along with disciplinary measures, he said he would require each medical center director to verify in writing that they are complying with agency guidelines.
The VA says the problems were caused by human error in the cleaning and operation of endoscopic equipment.
At the Murfreesboro facility, for example, officials believe medical staff mistakenly used a two-way valve that may have allowed bodily fluids to enter a part of the scope that was believed to be sterile.
Several top VA officials with experience at private hospitals said similar discoveries in the private sector would not have been publicized without specific knowledge that a patient was harmed.
Daigh said his investigators tried unsuccessfully to get information about potential problems at private hospitals, and several lawmakers said they think the problem probably extends beyond the VA.
"If this is happening in VA, what is happening ... in our greater health system?" asked Rep. Steve Buyer of Indiana, the top Republican on the committee. "My sense is that there are some greater problems out there."