Thomas Moyer, 50, has been indicted along with two other officers from the Santa Clara Sheriff's Office by a grand jury, the District Attorney's Office in California said.
County undersheriff Rick Sung and sheriff's captain James Jenson are accused of requesting bribes for the permits.
Moyer currently serves as head of global security and has been working at Apple for nearly 15 years.
District Attorney Jeff Rosen said Sung, 48, is the highest ranking law enforcement official in the county that his office has ever prosecuted.
Carrying concealed firearms in California is illegal without a permit, and county sheriffs have broad discretion over their issuance, which can cost anywhere between $200 and $400.
Santa Clara County claimed that Sung did not issue the permits until Moyer agreed to donate the iPads.
But the donation was stopped at the last minute when Sung and Moyer learned that the DA's office had issued a search warrant to seize permit records.
Rosen said: 'Call this quid pro quo. Call it pay-to-play. Call it give to get. It is illegal and deeply erodes public confidence in the criminal justice system.'
Moyer's attorney Ed Swanson said his client was innocent of the charges.
Apple stated that it had conducted its own investigation and found no wrongdoing on the part of their chief security officer.
Swanson said Moyer had applied for weapons permits for some Apple security personnel to protect executives and employees after shootings at other Silicon Valley tech firms.
Back in 2018, a woman entered the headquarters of YouTube and shot three people before killing herself. Nasim Aghdam stormed into YouTube's campus south of San Francisco and shot into a crowd of employees eating lunch.
Swanson said of the new permit applications: 'They went through the process the way you're supposed to do it.'
He added that the donation of the iPads was not connected to the permits.
He said: 'There was no bribe, no quid pro quo.'
If found guilty, Moyer could serve prison time.
The scandal is the latest in an ongoing corruption probe by the DA into the Sheriff's Office over Sheriff Laurie Smith's 2018 re-election campaign.
Thus far, six people have been indicted in the investigation involving deals involving gun permits for political favors.
Insurance broker Harpreet Chadha, 49, allegedly offered $6,000 worth of luxury box seat tickets to a San Jose Sharks hockey game in exchange for gun permits.
Sheriff Smith then used the luxury box to celebrate her reelection with family members and some of her biggest political supporters.
That case did not involve Apple, although campaign finance records show Moyer donated $1,000 to Smith's 2018 campaign shortly prior to receiving the permits.