Somalia's semi-autonomous region of Puntland has protested to Ethiopia, accusing its forces of carrying out a cross-border undercover operation.
Puntland's security minister told the BBC two people were in hospital after Ethiopian forces entered Galkayo town at night and raided a house.
He said Ethiopian officers had shot one man and abducted another, later dumping him by road with a bullet wound.
Ethiopian forces were in southern Somalia until they withdrew in January.
Puntland Security Minister Abdullahi Said Samatar said the forces must have crossed over from Ethiopia's Somali region, also known as the Ogaden, where rebels are fighting the government.
But he said until a police investigation was finished it was not possible to say if it was connected to the unrest in the Ogaden.
"Our relationship with Ethiopia has always been good, but we cannot accept security forces intervening in this way," he told the BBC's Somali Service.
Rebels seeking independence for the Somali-speaking population in Ethiopia have operated in the Ogaden since 1984.
Correspondents say they seemed to get a new lease of life when Ethiopia troops went into Somalia to oust the Islamist administration from Mogadishu in late 2006.
Earlier this year, Ethiopia withdrew but Islamist groups now dominate much of southern and central Somalia, with a UN-backed government restricted to parts of the capital.
Puntland has been an ally of Ethiopia since it broke away to run its own affairs in 1998, seven years after Somalia descended into clan warfare.
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