Islamist fighters seized the officer on Sunday in clashes that killed at least 51 people, 48 from the Juba Valley Alliance (JVA) militia and three Islamists, an official with movement said in this key southern port.
The claim came a day after the Islamists' supreme leader called for the start of a long-threatened "jihad," or holy war, against Ethiopia, which is alleged to have sent troops to support the Somali government.
"We have arrested an Ethiopian officer," Islamist spokesman Sheikh Shukri Abraham told reporters in Kismayo, about 88 kilometres (53 miles) south of the scene of Sunday's fighting in the town of Buale.
"He told us when we interrogated him that there are at least 200 men from Ethiopia and they were sent by the Ethiopian government to assist the (Somali) transitional federal government," he said.
"They are on some kind of secret service in Somalia," Abraham said.
He would not reveal the name or identity of the captured man but said he would be displayed in public along with military equipment and vehicles taken from the JVA, which is led by the defence minister in the government.
Ethiopia and the government have repeatedly denied eyewitness accounts of Ethiopian soldiers in Somalia, although Ethiopian Prime Minister Meles Zenawi has said several times that Addis Ababa has deployed trainers and advisers.
There was no immediate reaction to the claim from mainly Christian Ethiopia, which has vowed to protect itself and the Somali government from the "jihadists."
Fighting in Buale flared on Sunday when members of the JVA, which has vowed to re-take Kismayo from the Islamists who seized the port last month, clashed with Muslim gunmen, according to witnesses.
On Sunday witnesses reported at least five deaths but on Tuesday, Abraham said the toll had been much higher, with 48 JVA and three Islamist fighters killed and numerous injuries on both sides.
He added that the Islamists had seized 38 "battlewagons," machine-gun mounted pick-ups also known as "technicals," from the militia.
"We won the battle and we shall continue fighting until we finish those who are against the Islamic courts," Abraham said.
On Monday, the chief of the Supreme Islamic Council of Somalia (SICS), a cleric designated a "terrorist" by the United States, urged all Somalis to immediately take up arms against Ethiopian troops.
"Their graves will be littered everywhere in Somalia," Sheikh Hassan Dahir Aweys said in a speech to mark the end of the Muslim holy month of Ramazan in Mogadishu, which the Islamists seized in June from warlords.
Also Monday, the Islamists re-took a town near the temporary government seat of Baidoa, about 250 kilometres (155 miles) north-west of Mogadishu, that witnesses said was occupied on Saturday by government and Ethiopian troops.
The deteriorating situation threatens to scupper a planned third round of Arab League-mediated peace talks between the government and the Islamists set to begin on October 30 in Khartoum.
Somalia has been without a functioning central administration since 1991 and the government, formed in neighbouring Kenya in 2004, has been wracked by infighting and unable to assert control over much of the country.

Copyright AFP (Agence France-Presse), 2006