The London-listed company’s Tanzanian arm was found not have paid pay roll and property taxes as well as airport departure charges from January to November last year.
In a tax audit last month the Tanzanian taxman found the company owed 1.9bn Tanzanian shillings and $252 700. With interest and fines, the total sum owed came in at 2.8bn shillings (£1.1m) and $651 300 (£414 200). The sums do not take into account any corporation tax the company may owe.
"Fastjet works closely with the Tanzanian government to properly address all historic issues relating to tax,” the spokesperson said.
The claim is the latest in an array of other demands and legal cases that the carrier is embroiled in. These include disputes in Kenya and Uganda.
Fastjet enters the SA aviation market
In December, Fastjet signed an option agreement with 1time Airlines parent 1time Holdings to buy all issued share capital in the defunct airline for R1.
The low-cost, Africa- focused airline promised travellers they could expect low airfares when it enters the South African market.
Before it went under, 1time was the second-largest low-cost airline in the country.