"We believe it was a knife," the sheriff told reporters.
The video, filmed by a neighbor, shows suspect Gilbert Flores acting "wildly aggressive," a source with knowledge of the investigation told CNN. The footage also shows the suspect charging one officer with a knife at one point and also shoving chairs at an officer, the source said.
But authorities aren't releasing the second video and also declined to comment on whether they found a knife at the scene where Flores was shot, the sheriff said.
The second video will be examined by the Texas Department of Public Safety's crime lab, which will "try to enlarge and slow down the sequence" so investigators can get "a better idea of exactly what he had in his hand," the sheriff said.
Meanwhile, the FBI opened a federal civil rights investigation into the incident "to determine whether a civil rights violation took place as a result of a deputy willfully engaging in the use of excessive or unjustified force," the agency's San Antonio office said Wednesday.
The first video, shot by a bystander, was made public by a San Antonio TV news station and provides a stark, long-distance view of Flores with his hands up in the air before he was shot last week. The sheriff said both deputies fired their guns but declined to state how many times.
The second video covers a longer period and is recorded from a different angle than the cell phone video that has been shown by the news media. Deputies were responding to a domestic violence call.
Asked whether the second video showed Flores with both hands up when he was shot, Pamerleau stated, "We saw that."
She then reiterated remarks she made last week: "As I mentioned in the press conference on Friday evening, that video causes us concern."
One of the two deputies tried to use a Taser on Flores, but the device's probes did not make contact with him and failed to subdue him, the sheriff said.
When a reporter asked why the other deputy did not deploy a Taser, Pamerleau responded, "I don't know that." She said all her department's patrol officers carry Tasers.
The deputies, who are on administrative leave, are Greg Vasquez and Robert Sanchez, the sheriff's office said.
CNN's efforts to contact them have so far been unsuccessful.
Each has been with the sheriff's office for more than a decade, Pamerleau said.
A 'troubling' video
The source with knowledge of the investigation told CNN on Wednesday that the second video shows Flores holding a knife as he is shot.
The source added that the suspect had both hands up, but he held a knife in one of his hands.
The suspect had been yelling and antagonizing police, and a voice on the video speculates whether the suspect is trying to get killed, the source said. That voice doesn't belong to the police officers or the suspect, the source said.
The source added it's hard to understand what the suspect says on the video because he is yelling loudly.
Bexar County District Attorney Nicholas LaHood told CNN the second video is "a better view to make an assessment on what happened. It is a closer view and a better angle."
He also characterized the second video as "troubling," and said the FBI has joined the investigation into Flores' death.
U.S. Rep. Joaquin Castro, D-Texas, who represents the area, urged that the second video be made public.
"I hope the Bexar County Sheriff's Office will release the second video in the Gilbert Flores shooting as soon as possible," he tweeted Tuesday.
Who took first video
The first video was taken by Michael Thomas, who was taking a quick break from his job working on a house in a neighborhood outside San Antonio, Texas, when he noticed a commotion.
Ambulances and police cars had pulled up at a nearby home.
He thought, "There's a lot of things going on in the world," he told CNN on Wednesday, and he decided he'd do what he had seen so many other people in the news doing lately. He pulled out his cell phone, ready to record if needed.
"It happened so fast," Thomas said.
Standing across the street, Thomas saw -- and recorded -- two Bexar County sheriff's deputies and a shirtless man. In the video, the man, Flores, raises at least one hand in the air and is then shot and falls on his back.
"Why did they shoot him?" Thomas said on CNN's "New Day."
The man, from what Thomas could see, "wasn't attacking" the officers. "At the time he was shot, it didn't look like he was posing a threat at all."
"As the guy and police were going back and forth, the man acted like he was going to run back inside his house, and then ran around the cars by the cop car, and the cops started pursuing closer to him," Thomas said.
Because Thomas' video is shot from a distance across a street, it's impossible to hear what the officers or Flores might have said.
Thomas told CNN that he "assumed the man had both hands up but he did not actually see that," he said. In his video, the man's left arm is obscured by a utility pole.
A domestic violence call
Thomas told CNN's "New Day" that after he finished recording the four-minute video, he went back to work and told co-workers about it. They urged him to give it to the media.
It didn't make sense to him to hand over what he'd captured to police, he said.
CNN affiliate KSAT
first broadcast the video Friday but didn't show Flores' death on air, and CNN obtained the footage.
The incident comes at a time when law enforcement officers are under scrutiny
for how and when they resort to lethal force. The killings of several people by police over the past year have heightened tensions with the communities they serve, especially among minorities.
Authorities were called to Flores' home Friday for a report of domestic violence. Dispatch communication shows that a woman in the house had a gash on her head and that her baby may have been injured, too.
Flores resisted arrest, authorities say
Pamerleau said Flores resisted arrest. Nonlethal force -- stun guns and shields -- was used to try to subdue him, but those methods didn't work, she said.
"Certainly what's in the video is a cause for concern," she said. "But it's important to let the investigation go through its course so we can ensure a thorough and complete review of all that occurred."
Pamerleau said both deputies fired shots after a "lengthy confrontation."
Flores had previous run-ins with the law. He was cited for possession of marijuana in 1995, criminal trespassing and aggravated assault in 1999, and aggravated robbery in 2003.
'Threats to our deputies' lives'
KSAT posted the entire video on its website on Monday and included a viewer warning in the story that contained the recording. KSAT later explained in an online post
why management decided to show the full video online.
"Providing the video on KSAT.com allows for viewers to make their own decision on whether to click on a link to see the video," the station said.
KSAT said the only edits to the recording were to remove offensive language from Thomas.
The station told the sheriff's office about the video and sent it there, but the station did not give any warning that it would post the entire raw video Monday, said James Keith, media relations officer for the Bexar County Sheriff's Office.
Now, Keith says, the sheriff's office is worried about the safety of its deputies in light of the video's public release. On Monday, it tweeted a statement that said "broadcasting a man's death for $100 sparked threats to our deputies' lives. Let KSAT know what you think."
In a post on its website
, KSAT explained its decision to show the video and the discussions station management had with Thomas.
"Before sharing the video with us, Thomas asked for payment. While most viewers share video with us at no charge, we agreed to pay Thomas a $100 licensing fee for the video. It is not uncommon for news organizations to pay for video from freelancers or citizen journalists."
The station said it was making no judgment about the officers' actions, but it was obligated to share "information in the public interest."
Deputies wear civilian clothes
When asked about the sheriff's office tweet, Keith cited the case of Darren Goforth
, a deputy who was shot from behind and killed while filling up his car at a gas station.
"After what happened in Harris County, we are not going to take any chances," he said. "Now our deputies are coming to work in civilian clothes because of their concern for safety."
Hours later, the sheriff's office sent out a message with the following statement: "In regards to the deputy-involved shooting, we're asking for calm and patience. We are diligently working to complete the investigation so we can move to the next step. We want to get this right for the Flores family, our deputies and our community."
More officer cameras
The administrative body in Bexar County, the Commissioners Court, on Tuesday approved a budget that included 185 cameras for the sheriff's office.
Thirty-four of the units can be used as a dashboard recorder and a body camera.
Neither deputy involved in the shooting was wearing a body camera.