Kenya Airways says its staff in the Democratic Republic of Congo who were released on Monday had been detained because of a "misunderstanding" by the authorities.
The airline says it is resuming flights to the country - which it had suspended - after the "unconditional" release of the two employees.
The staff were detained last month allegedly because of missing customs documents concerning what was described as valuable cargo.
The airline maintains that its staff were innocent.
The airline's managing director, Allan Kilavuka, told the BBC's Newsday programme that the cargo in question was made up of banknotes from a Congolese bank that were being transported to the US.
Mr Kilavuka said the airline had not taken custody of the cargo at the time its two staff members were arrested.
However, the authorities seized the money and detained the employees, he said.
"This was purely a misunderstanding by the military intelligence officers," Kenya Airways managing director said.
He added that they had tried to explain multiple times "that we had not taken custody of the money but they wouldn't listen".
"So my only assumption is that there was clear miscommunication - may be between the military officers and the custom officers in Kinshasa," he said.
Congolese officials have not yet commented on the matter.
The continued detention prompted Kenya Airways to suspend its flights, saying the situation had made it difficult to support flights.
Last week it said it was co-operating with investigating agencies and government entities in DR Congo and Kenya to resolve the matter.
The airline has now lauded all the efforts made to ensure the release of the staff, including by government officials and the embassy in Kinshasa.
It says flights are due to return from Wednesday, now “with the necessary ground support in place”.
Mr Kilavuka said he would also be travelling to Kinshasa to ensure the matter is properly resolved.
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