Men from the Murle community, who crossed into Ethiopia, are being blamed.
Feuding communities on both sides of the border have been known to attack each other, often carrying away spoils.
A similar incident last April prompted Ethiopia’s army to cross into South Sudan in a hunt for kidnapped children.
The latest raids were carried out over two days – first on Sunday and then Monday – in Gambella’s Gog and Jol areas, which border South Sudan, Chol Chany, a spokesman for the Gambella region, is quoted by Reuters as saying.
“Murle bandits carried out the attack. They fled along with 43 children,” Mr Chany said.
Last year’s incidents in which 100 Ethiopian children were kidnapped was also blamed on members of the Murle community.
At that time, residents of Gambella town demonstrated, demanding justice and calling for better security.