The surveillance cameras at three of the key subway stations where the shooting took place were discovered to be not working.
The MTA hasn't responded to 7 On Your Side Investigates questions as to what went wrong.
The MTA spent millions of dollars on 10,000 cameras at all 472 subway stations in New York City.
"We have incredible coverage throughout the system and especially on this line," said Janno Lieber Wednesday of the system's surveillance system.
But the system wasn't incredible for the investigation on Tuesday.
In an appearance on CNN Wednesday night, MTA Chair and CEO Janno Lieber said there were "a couple of cameras that definitely had internet hookup linkage problems," but says that the NYPD combed through video up and down the line.
He says there were 600 cameras on that one line in Brooklyn that recorded material that helped the department "a great deal."
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The MTA cameras picked up a surveillance image of the mass shooting suspect wearing a vest and hard hat while entering the subway and Kings Highway, but police say the video was not streaming at the three locations after he entered and opened fire.
"We're still investigating that to see why or how, whether it was a mechanical problem or electrical issues, why those videos weren't up," said James Essig, NYPD Chief of Detectives.
The cameras are bought, operated and maintained by the MTA.
"It doesn't sound right," said Professor Robert Paaswell, who's the former head of the Chicago Transit Authority and a transportation and civil engineering expert.
"It's a screw up, it's a real screw up," Passwell said. "If the person who's responsible for that worked for me at the CTA, they'd no longer be working for me at the CTA."
"It's the IT person's job to make sure the system works perfectly, they should make system checks every morning, they should randomly go through the stations, they should continue the random checks throughout the day," Paaswell said.
7 On Your Side asked the MTA repeatedly Wednesday what caused the outage and how many other cameras aren't working and have received no specific responses.
"Our video has been a source of investigation for the NYPD and they continue to comb through other video because they're trying to track him through the system in New York," Lieber said.
The state comptroller audited the city's cameras a few years ago, telling the MTA it could do a better job of maintaining the system.
The MTA made a series of improvements but the 2019 report shows it did not follow the first two recommendations: to provide better camera training to new employees and to focus resources on meeting preventative camera maintenance targets.
It's unknown if any additional changes or improvements have been made since then.
"The subway system is the lifeblood of New York and we really need the mayor and the governor to be able to make good on the commitment they've made to public safety," Lieber said.
The MTA has both live streaming and recorded video. Eyewitness News learned hundreds of NYPD detectives reviewed hours of footage overnight and have identified at least three images of the suspect so far.
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