By Katy Migiro

NAIROBI, March 23 (Thomson Reuters Foundation) - A nine-year-old girl was among hundreds of child soldiers freed in South Sudan over the last three days, part of the largest ever release of child fighters in the world's youngest nation, the United Nations said on Monday.

It is the third release by the South Sudan Democratic Army (SSDA) Cobra Faction since its leader David Yau Yau signed a peace deal with the government in May.

On Saturday, 654 children were registered with the U.N. Children's Fund (UNICEF), bringing the total number of children freed by the militia group since January to 1,314.

"Because there are so many of them, it became impractical to release them all on one day," John Budd, a spokesman for UNICEF in Juba, told the Thomson Reuters Foundation.

Some 250 children, including four girls, were released on Saturday, with the remainder freed on Sunday and Monday. The children exchanged their weapons and uniforms for civilian clothes at a formal ceremony in Lekuangole, a town in Pibor County in Jonglei State, UNICEF said.

The group, which operates in restive Jonglei State, has told UNICEF that it will free up to 3,000 children in total.

UNICEF is providing the former fighters with food, shelter and psychosocial support while it traces their families.

Of the 660 children freed in earlier demobilisations, 200 have been reunited or are close to being reunited with their families, UNICEF said.

Several militias have been fighting the government since South Sudan won independence in 2011 after decades of war with Khartoum.

Civil war began in the world's youngest country in December 2013 after fighting erupted in the capital, Juba, between soldiers allied to President Salva Kiir and those loyal to his former deputy, Riek Machar.

More than 12,000 children have since been recruited into armed groups, UNICEF said.

In February, at least 89 boys were abducted by an armed group while sitting exams near Malakal in Upper Nile State. Boys older than 12 years of age were taken away by force, UNICEF said.

"While we welcome freedom for the children, we are also deeply disturbed by the hundreds of children being abducted in Upper Nile and Unity States," UNICEF's country representative, Jonathan Veitch, said in a statement.

"Boys are being targeted and rounded up by forces of the government and opposition."

South Sudan is one of seven countries where UNICEF is campaigning to end the recruitment of children as soldiers, following a government commitment in 2009 to stop using children as fighters.

(Reporting by Katy Migiro; Editing by Alex Whiting)