Somali warlord Muse Sudi Yalahow has threatened to shoot down any plane flying over the capital, Mogadishu, known to be diverted to other towns.
The leaf narcotic, khat, and other commodities, arrive by air
This follows a deal reached by the prime minister with Kenya to close airstrips controlled by the warlords.
Flights from Kenya would have to fly over Mogadishu to reach his government faction based in Jowhar town.
The airstrips been an important source of revenue to rival warlords since the central government collapsed in 1991.
Some 10 plane loads of the mild narcotic leaf, khat, arrive in Mogadishu every day.
Prime Minister Ali Mohammed Ghedi told the BBC the decision to close the airstrips had been taken to bring law and order to Somalia.
The country has been without a functioning national government for 14 years and a transitional parliament and government, sworn in last year, has failed to end the anarchy.
Mr Ghedi and the president have made Jowhar, 90km (56 miles) north of Mogadishu, the temporary capital for their government as they say Mogadishu is unsafe.
But the speaker of parliament has set up operations in the capital, along with former Mogadishu warlords, including Mr Yalahow who is also the trade minister in new the government.