Prosecutors allege the officials used a false bomb threat to divert a Ryanair flight to the Belarus capital, where opposition journalist Roman Protasevich and his partner were detained.
FBI officials said the incident was a "reckless violation".
Earlier this week a UN report concluded the bomb threat was deliberately false.
A spokesperson for the US Justice Department said the four men, Leonid Mikalaevich Churo and Oleg Kazyuchits - the director general and deputy director general of Belarus' state air navigation authority - and state security officers Andrey Anatolievich Lnu [Last Name Unknown] and Fnu [First Name Unknown] Lnu, remain at large in Belarus.
If they were tried in a US court they would face a life sentence.
According to the charges, Mr Churo personally communicated the false bomb threat to Belarusian air traffic officials before the Ryanair flight to Vilnius in Lithuania took off from the Greek capital Athens.
The air traffic officials waited for the plane to enter Belarusian air space before alerting the pilot to the purported bomb threat in order to force it to land in Minsk.
Mr Churo's deputy, Mr Kazyuchits, later attempted to have the incident record falsified to hide the bomb threat and the involvement of state security officials, the indictment alleges.
Speaking after the charges were filed at a federal court in New York, FBI Assistant Director Michael Driscoll called the hijacking a "reckless violation of US law".
"The next pilot who gets a distress call from a tower may doubt the authenticity of the emergency - which puts lives at risk," Mr Driscoll added.
Last year, Ryanair CEO Michael O'Leary referred to the incident as a "state-sponsored hijacking".
The incident sparked international outrage and punitive sanctions were imposed on Belarus by the US, EU and the UK.
At the time, Belarusian president Alexander Lukashenko insisted the bomb threat had been real and he was "thinking about the country's security".
Mr Protasevich, a 26-year old journalist with the Nexta opposition media, and his partner Sofia Sapega were detained once the flight had landed in Minsk.
Mr Protasevich was released from prison in June and has spent the past seven months under house arrest.
His parents told Belarusian media in November that their contact with him has been intermittent since his release.
Mr Lukashenko - who has ruled Belarus since 1994 - claimed victory in a widely discredited presidential election in 2020, sparking months of mass protests.
He has since launched a brutal crackdown on dissenting voices who challenged his win.