MSF-Holland later confirmed that three of the dead were working for the aid agency - a Frenchman, a Kenyan doctor and a Somali driver.
Kismayo, a key port, is under the control of the local clan leaders, not Somalia's interim government.
The interim government has fought a year-long battle with Islamic fighters in the capital Mogadishu.
The government and its Ethiopian allies have been frequently targeted by roadside bombs and ambushes.
During a two-week offensive in late 2006 and early 2007, Ethiopian and Somali forces battled the opposition fighters near Kismayo and further south, towards the Kenyan border.
Islamic fighters have threatened to launch attacks in Kismayo as part of an attempt to establish Islamic rule across Somalia.