Kenya has banned all flights to Somalia, citing security fears.
Some 20 tons of khat are flown to Somalia each day
The ban comes two weeks after the US issued a warning about suicide attacks from Islamist militants in Somalia.
Kenya is the main entry point for international travel to Somalia and is also the source of much of the popular stimulant khat, consumed in Somalia.
There were protests earlier this year when the Islamists who control much of southern Somalia banned the sale of khat during the holy month of Ramadan.
Khat is chewed by many Somali men, especially the gunmen who have fought for control of the country for the last 15 years.
There were six flights a week from Nairobi to the Somali capital, Mogadishu, and services to three other towns and many more khat flights each day.
Kenyan khat, or miraa, growers have condemned the flight ban.
Maoka Maore, MP for the central Ntonyiri constituency, said that 20 tons of khat, worth $800,000 was sent to Somalia each day.
"Even if you close it for a week, the effects are going to be devastating," he told the BBC's Network Africa programme.
"All of our productive land is in miraa farms."
Stimulant, making the user more alert and talkative
After a few hours, it produces a state of calm
A chemical found in khat could boost the power of men's sperm
Long-term use can bring on insomnia, heart problems and sexual problems
Can bring on anxiety and aggression
The Islamists have tried to clamp down on the trade since their rise over the past five months.
They banned its sale during the Muslim holy month of Ramadan, sparking street protests in Kismayo.
In weekend fighting, the Union of Islamic Courts (UIC) say they have taken control of the town of Bandiradley, near the border with the Puntland region.
Witnesses said at least eight people were killed in the fighting.
Semi-autonomous Puntland has escaped much of the anarchy, which has ravaged southern Somalia since 1991.
On Saturday, Somalia's transitional government dismissed a peace deal between parliamentary speaker Sharif Hassan Sheikh Adan and the UIC, saying the speaker did not have the mandate to reach a deal on the government's behalf.
There are fears of a regional conflict starting in Somalia, as Ethiopia backs the government and its rival Eritrea is accused of arming the Islamists.
Ethiopia denies having fighting forces in Somalia but admits to having hundreds of military trainers, while Eritrea denies backing the UIC.
The government, formed at peace talks in Kenya, only controls the territory around the town of Baidoa.