The Somali government wants the Kenya Defence Forces to immediately withdraw from the port town of Kismayo.
On Sunday at a press conference in Mogadishu , deputy Information minister Abdishakur Ali Mire called for "a more neutral African Union force."
A press release from the Prime Minister's office said that "the AMISOM Section Two forces (KDF) supported one side of the two fighting factions" during three days of fighting recently for control of the port.
"Amisom Section Two forces purposefully arrested government appointed division 43 SNA commander, Col. Abbas Ibrahim Gure," Abdishakur Mire said.
"We are also informed that there was a targeted offensive against civilians and the SNA command center in Kismayo by the Amisom Section Two forces, which is unfortunate."
The minister called for "the immediate replacement of AMISOM Section Two forces to a more neutral African Union force" as well as the release of Col Gure.
He also called for a fact finding mission and the appoint of an African Union political officer in Kismayo who is not a member of the KDF.
Kenya allegedly detained Col. Abbas and transported him to Wajir for questioning on suspicion that he was involved in a roadside bombing that led to casualties of Kenyan soldiers in Kismayo.
Abbas was the leader of a militia from Gedo who earlier this year was appointed as the commander for Jubaland, teh region of southern Somalia where Kismayo is the largest city.
Last night KDF spokesman Colonel Cyrus Oguna dismissed the minister's criticism as baseless.
"The official who issued that report should have checked with KDF if truly we were holding the commander or not. We had facilitated the commander's movement but the plane that was carrying him was forced to land in Doble due to mechanical problems. The commander left Doble by the time the statement was being issued," said Oguna.
"KDF is in Somalia courtesy of AMISOM which has been invited by the government. We are neutral," added Oguna.
He said the KDF was in Kismayo to "promote security and help in the rebuilding of Somalia which has suffered decades of civil unrest.
KDF operating as Section Two of the African Union Mission in Somalia (Amisom) forces. Uganda makes up the bulk of the Section One force and has overall command of Amisom. Amisom also has troops from Burundi and Sierra Leone.
KDF entered in Somalia in February 2012 under Operation Linda Nchi to deal with al Shabaab militia and formally joined Amisom in July 2012. KDF took over Kismayu from al Shabaab in September 2012.
But the Somali government believes the KDF of been siding with Sheikh Ahmed Madobe to create a semi autonomous state of Jubaland. Madobe, the commander of the Ras Kamboni Brigade which was fought with the KDF against al Shabaab, was recently elected president of Jubaland.
"The only role that Kenya and Ethiopia have played is the provision of troops who have helped in flushing out the Al Shabaab elements from Jubaland," Madobe said recently.
"KDF transited into Amisom and there have been no incidents of human rights abuse by either KDF or Amisom," Madobe said.
Kismayo is strategically important for Kenya, which needs a friendly buffer zone at its border with Somalia.
The rival militias struggling for control of Kismayo are mainly interested in gaining control of the port which previously was under the control of al Shabaab.
There is a large income from illegal charcoal exports to the Gulf States, according to the UN. There are also substantial imports of sugar, rice and other commodities through the port that are finding their way duty free into Kenya.
The UN Security Council is expected to release a report on Kismayu port on July 12 that will claim that Ras Kamboni, KDF, and al Shabaab are also still profiting from business in Kismayo port.
Last week a second bout of fighting erupted between Ras Kamboni and a rival militia led by Barre Hirale who is also claiming to be the president of Jubaland.
However, neither he nor the other four clan leaders claiming to be president have the backing of the central Somali government in Mogadishu.