By Hereward Holland

JUBA (Reuters) - An estimated 3,000 South Sudanese rebels have surrendered and accepted an amnesty, a government official said on Friday, ending a long-standing insurgency in the oil-producing north of the country.

South Sudan's government has been struggling to contain several insurgencies it claims are supported by its old civil war foe Khartoum since it gained independence from Sudan in July 2011. Sudan denies the claims.

Relations between the Sudans have thawed in recent months, paving the way in April for the resumption of the South's oil being piped through Sudan after a 15-month shutdown.

On Friday, South Sudan's President Salva Kiir issued an amnesty for six rebel commanders including Bapiny Monytuil, the leader of the South Sudan Liberation Army (SSLA), and their troops.

"The (SSLA) militia that have been in the north have surrendered. All of them have come," Unity State government spokesman Joseph Arop Malual told Reuters. Unity contains several oilfields.

Led by a senior commander, Matthew Puljang, a large group of SSLA crossed the border with around 100 trucks from Sudan, where they are believed to have a training base, Malual said.

The SSLA, formed in the late 1990s, is one of largest rebel groups in the region. It switched sides several times during the civil war between north and south Sudan that killed some 2 million people in fighting over oil, religion, ideology and identity. The war, which began in 1983, ended with a 2005 peace deal that paved the way for the southern secession.

"(The surrender) is positive because they are our brothers. We no longer have to fear attacks from the north," Malual said.

There was no immediate comment from Sudan or the SSLA, which has accused the South Sudan government of corruption in the past.

Security analysts say hundreds of people were killed in clashes between the predominantly ethnic Nuer SSLA and government forces in November 2011 and March 2012 in Unity State, although the group has not been active recently.

Earlier this month Sudan's President Omar Hassan al-Bashir made his first visit to South Sudan since its secession in a bid to help normalize relations and restart cross-border trade.

"(This) is a significant development toward improved relations between Sudan and South Sudan. It shows that concrete deals were signed during Bashir's recent visit to Juba," said Jonah Leff, a regional analyst for the Geneva-based Small Arms Survey, referring to the surrender.

(Editing by Hugh Lawson)