Salman is expected to appear in court Tuesday in Oakland, according to Assistant US Attorney Abraham Simmons.
The federal charges were filed in the Middle District of Florida, according to a law enforcement official. The arrest was first reported by The New York Times.
Authorities believe Salman acted of her own free will and knowingly took steps to obstruct the investigation into the massacre, according to a law enforcement official.
The official said Salman's claims that she was coerced through her husband's abusive behavior did not stand up. Another official says the evidence will show that she was complicit and knew her husband was going to do something bad.
Her attorney said Salman had no prior knowledge that her husband would enter the Pulse nightclub in Orlando and commit the deadliest mass shooting in US history.
"Noor Salman had no foreknowledge nor could she predict what Omar Mateen intended to do that tragic night," said family attorney Linda Moreno of Tampa, Florida, in a statement.
"Noor has told her story of abuse at his hands. We believe it is misguided and wrong to prosecute her and that it dishonors the memories of the victims to punish an innocent person."
CNN's Dan Simon visited her family's home in Rodeo, California, for reaction and was told "no comment."
Orlando police chief: 'She could've prevented this'
"I am glad to see that Omar Mateen's wife has been charged with aiding her husband in the commission of the brutal attack on the Pulse nightclub," said Orlando Police Chief John Mina.
"There's no doubt in my mind, based on the information I knew and I received from the FBI over the past seven months, that she knew, that she aided and that she could have prevented this tragedy," he told CNN's Erin Burnett.
Salman, who married Mateen in 2011, came under increasing scrutiny as authorities investigated Mateen, who killed 49 people
and injured more than 50 others when he opened fire at Pulse, a gay nightclub in June last year. The gunman was killed after barricading himself in a bathroom at the Orlando club.
A law enforcement official told CNN
last year that authorities were looking into whether Salman should face charges.
What she said
Salman gave conflicting accounts about what she knew of Mateen's intentions in the hours before the attack, authorities said
. Salman told the FBI her husband said he wanted to carry out a jihadist attack. But she denied knowledge of his plans, a law enforcement official told CNN last year.
Months before the attack, Mateen added the name of his wife to his life insurance policy and made sure she had access to his bank accounts, two law enforcement officials said. The gunman transferred his share of the home, in which his sister and brother-in-law lived, to them for just $10. Mateen also bought his wife an expensive piece of jewelry, the sources said.
Salman told investigators that in the weeks leading up to the attack, Mateen spent thousands of dollars, buying among other things the guns used in the massacre. In April, he visited Disney World with his wife, and Disney security officials believe he was conducting surveillance, a law enforcement official told CNN.
Two days before the attack, he left his house angry and was carrying a bag of guns. Salman begged her husband not to leave and grabbed him by the arm, she said.
Two hours after the attack started, Mateen texted his wife at 4 a.m. and asked her whether she heard the news about the shooting. At one point, Salman told Mateen that she loved him.
Mateen's ex-wife, Sitora Yusufiy, last year described a brief but violent relationship to a man whom she was only able to escape through her family's help. She said he was physically abusive and a steroid abuser.