A senior official told the BBC hundreds of people had been wounded and more than 200 abducted, mainly children.
The clashes took place on Thursday when members of the Murle group are said to have attacked the majority Lou Nuer, stealing nearly 40,000 cattle.
Jonglei is one of the newly-independent country's least safe areas.
The fighting took place, according to several sources including the state governor, when young Murle men attacked several locations inhabited by the Lou Nuer in and around the town of Pieri. Much of the town has apparently been burnt down.
The Murle were apparently seeking revenge for a recent attack by the Lou Nuer.Security challenges
The state's minister for law enforcement, Gabriel Duot Lam, also said an estimated 38,000 cows had been stolen by the Murle.
Earlier, state governor Kuol Manyang told the BBC the attack was a cattle raid, and a consequence of poverty and competition over resources.
"People need cattle for their own survival, for food security and for marriages - and there is competition over land and water resources, because of underdevelopment," said Mr Manyang.
The BBC's James Copnall, in the Sudanese capital Khartoum, says cattle rustling frequently leads to bloody clashes in the state and elsewhere in South Sudan.
The attack is the latest in a string of deadly incidents between the Murle and the Lou Nuer. Hundreds of people die in inter-ethnic clashes in Jonglei each year.
The Murle are often accused of stealing children, allegedly because they do not have many of their own.
South Sudan has been independent for just over a month, and faces serious security challenges, particularly in Jonglei.
Many civilians are armed and the poor roads make it difficult for the security forces to move around the state.
But a representative of the Lou Nuer community has expressed his anger, saying the government of South Sudan was failing to provide security for its people.