David Henderson faces charges for two offences under the Air Navigation Order, the Civil Aviation Authority (CAA) said.
The 66-year-old is accused of acting in a “reckless/negligent” manner, and being involved in the commercial use of the plane involved in the crash.
Henderson is alleged to have arranged the flight which crashed into the sea in January 2019.
CAA director Richard Stephenson said: “The UK Civil Aviation Authority has commenced a prosecution of David Henderson for offences associated with the fatal light aircraft accident over the English Channel in January 2019.
“It will be inappropriate for the CAA to say anything further until the case is concluded.“
Sala, 28, from Argentina, had been signed by Premier League side Cardiff from French club Nantes for a club record fee of £15m.
He was making his way from France to Wales in a US-registered Piper Malibu PA-46 aircraft when it crashed. His body was found in the wreckage off Guernsey but the body of the pilot, David Ibbotson, 59, from Crowle, Lincolnshire, was never found.
A final report into the crash by the Air Accidents Investigation Branch (AAIB) published in March this year said the aircraft crashed “probably while manoeuvring to avoid poor weather”.
Investigators found the single-engined aircraft “suffered an in-flight break-up while manoeuvring at an airspeed significantly in excess of its design manoeuvring speed” - an airspeed limit determined by the aircraft designer.
Ibbotson was also likely to have been suffering from the effects of carbon monoxide (CO) poisoning, the report said.
The six-seater aircraft, which had only two people onboard, disappeared from radar shortly after 8.15pm and struck the sea 22 nautical miles north-west of Guernsey.
Neither the pilot nor aircraft had the required licences or permissions to operate commercially, the AAIB said.
Henderson appeared in court last month and was bailed to appear at Cardiff Crown Court on 26 October.
The prosecution could further delay the inquest into Sala's death.
Daniel Machover of law firm Hickman and Rose - which is representing the footballer's mother, Mercedes Taffarel - said: ”Mercedes Taffarel welcomes the prosecution of David Henderson, but is disappointed that it has today resulted in what may be a further significant delay to the inquest into Emiliano's death.
“This coming January will mark two years since the plane Emiliano was travelling in crashed into the English Channel.
”His mother remains desperate to know the full truth about how this could have been allowed to happen, and urges the CAA to proceed with its criminal prosecution as swiftly as possible, so an inquest can be held to establish this, and that similar deaths are prevented.”
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