South Sudan has stopped operations of Kenyan airline Fly540 at Juba airport over a protracted landing fees row, leaving travellers with only two direct flights between Nairobi and Juba.
Things came to a head on Tuesday August 14, when a Fly540 flight with 40 passengers on board left Nairobi for Juba at 4:45pmw.
With a flight time of one hour and 35 minutes, the passengers expected to land at 6:20pm. But this was not to be.
Barely half an hour into the flight, the pilot was informed by the airline's Juba airport manager that he no longer had landing rights, forcing him to fly back to Nairobi.
"We were surprised when the airline had to turn back almost half an hour into the flight. We were told that the South Sudan government had denied it entry. We were further informed that the airline had cancelled all its flights to Juba, hence our refunds would be processed given that the airline staff could not tell when they would be getting back the landing rights," an affected passenger told The EastAfrican.
Apparently, unbeknown to Fly540 staff at Juba airport, the South Sudan government had cancelled the landing rights for the carrier earlier that day, over what it called "accumulated landing fees." It is now two weeks since the airline suspended its operations in Juba.
"The Fly540 Juba airport manager only discovered this (cancellation) when he went to file the flight plan with Juba's civil aviation authority. He learned that the authority's director-general had issued an internal memo suspending the airline's landing rights," a source with knowledge of the developments told The EastAfrican.
The cancellation of landing rights was a culmination of a protracted back and forth between the management of Fly540, South Sudan's national security intelligence, the Ministry of Interior and the civil aviation agency, since April.
The EastAfrican has learned that on April 16, the South Sudan administration asked Fly540 to temporarily stop paying its landing fees following discovery of fraud within the civil aviation agency. Some of the agency's staff members were suspended from work and arrested.
"This was an active investigation and the airline complied with the instructions. However, the suspended staff from the aviation authority kept threatening the airline's Juba staff, which saw it seek protection services from Juba police," The EastAfrican was told.
On August 7, the Fly540 management was surprised to receive a letter from Juba's Intelligence agency (NISS) requesting payment of $27,000.
The letter asked that the money be given to some of the Intelligence agency employees who were in Nairobi on assignment.
"The Fly540 management asked for a letter from the civil aviation agency to support the request. This was, however, met with another demand letter now from South Sudan's Interior Ministry on the same day, demanding payment of the full arrears, which had clocked $123, 000," The EastAfrican was told.
The Fly540 management offered a payment plan, but this was declined. It is understood that South Sudan security officers on the same day raided the airline's Juba office and held staff hostage, demanding the payment.
"An agreement was reached that the airline would pay $50,000 upfront and the Juba office released $28,300 to the South Sudanese officials, upon which the staff members were released, with a promise to pay the balance in cash via a flight from Nairobi," The EastAfrican was told.
It is understood that the aircraft, which was turned away on Tuesday last week, had the balance on board.
"The matter of fraud is still an active investigation. The airline has no problem settling the arrears but is questioning the process because it is being bombarded by unethical requests from different agencies. It is something the Kenyan government and embassies are well aware of and are trying to resolve," a source with knowledge of the matter said.
It is understood that Fly540 and the Juba civil aviation agency have been in discussions since the suspension but nothing concrete has come out of the discussions.
The Kenya Civil Aviation Authority director general, Captain Gilbert Kibe, confirmed to The EastAfrican that his office was aware of the matter.
"Yes this is something that has been brought to my attention and we are investigating the issues they (Fly540) are having. I don't think I will comment beyond that," Captain Kibe said.
William Mwadime, a Kenyan consular official at the Kenyan Embassy in Juba confirmed that his office had reached out to the Juba authorities to try to resolve the matter.
"We had an informal session with Fly540 Juba management over the issue in the week of their flight suspension. We told them to file a formal letter on their concerns, which they did on Thursday. This was then shared with the Juba authorities and we expect feedback from them on Tuesday," Mr Mwadime said.
South Sudan, however, maintain that the decision to cancel landing rights was taken after the airline went into default on the payment of its landing fees, which according to Juba authorities had accumulated 'significantly'.
"You can seek the amount and default period from the airline management. What we want is these unpaid fees settled so that they can continue with their normal frequencies to Juba," an official at the South Sudan Civil Aviation Authority, who requested anonymity said.
Fly540, which operates two daily flights to Juba, suspended its services in July 2016 when the fresh fighting broke out, citing the deteriorating security situation.
The Nairobi-Juba route is now served by two daily direct flights by Kenya Airways, with RwandAir making a stop-over at Entebbe and Ethiopian Airline going through Addis Ababa.