Several cargo planes destined for Mogadishu are stuck in Nairobi with miraa worth about Sh50 million after Somalia suspended the flights.
But sources at the airport in Nairobi said some planes left for Kismayu, Puntland and Galkayo with miraa despite the ban.
Workers with some miraa exporting companies in the city had been told not to report to work from Monday. Some workers in fields in Nyambene were also told not to report until the issue was resolved. The companies complained of losses after Somalia's decision to suspend the flights.
No reason has been given for suspending the exports. Other officials said security matters could have informed the decision.
Somalia's Minister of Civil Aviation, Ali Ahmed Jangali, said they had decided to temporarily suspend all khat imports to Somalia from Tuesday.
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Officials at Jomo Kenyatta International Airport confirmed they had been notified of the suspension. The officials said at least 20 flights carrying miraa from Nairobi have been flying to Somalia daily.
Somalia is the largest market for the Kenyan stimulant plant largely chewed by Somalis and Arabs after several European countries banned the crop years ago.
A letter dated September 4 from Somalia's Civil Aviation and Meteorology Authority warned that violation of orders on Somalia airspace and disregard of the notice would have consequences.
"While considering special circumstances, Somali Civil Aviation and Meteorology Authority, on behalf of Federal Republic of Somalia, is hereby informing all miraa cargo operators and anyone it concerns that miraa cargo flights and its operations into Somalia have been cancelled effective September 6, 2016, until further notice," said the notice by the authority's general manager, Abdiwahid Ahmed.
The letter is copied to the Kenya Civil Aviation Authority and other Somali agencies and comes at a time when miraa farmers are struggling to find a stable market for their crop.
The government pledged to support the growers of miraa after it was banned in Europe. It is also banned in a number of other countries, including the US and Canada.