NAIROBI, April 21 (Reuters) - South Sudanese churches, political parties and voluntary groups pledged unconditional support on Thursday for a peace accord ending a civil war and called on armed groups backed by Khartoum to follow suit.

The move by about 20 influential civilian organisations widens support for a peace deal in January signed exclusively by the Islamist government of Khartoum and its southern rebel foes, ending 21 years of war in Africa's largest country.

Delegates at a three-day conference in the Kenyan capital Nairobi signed a covenant promising to "Unconditionally support the Comprehensive Peace Agreement" -- a deal that was criticised by many Sudanese at the time for excluding such groups.

Khartoum-backed southern militias who also fought in the war and which are seen as vital to the accord's successful implementation were invited to the discussions by the organiser, former Kenyan President Daniel arap Moi, but did not attend.

The north-south war ended by the January deal, between the Arabic-speaking Islamist government and southern animist and Christian rebels seeking greater autonomy, was complicated by oil, ethnicity and ideology.

The war killed an estimated two million people, mainly from famine and disease, but did not cover a separate conflict in Darfur where two years of fighting have created what the United Nations calls one of the world's worst humanitarian crises.

MILITIAS ABSENT

The absence of the militias from the meeting was criticised by many delegates, including those from the former southern rebel Sudan People's Liberation Movement/Army (SPLM/A) who alleged the groups had been forbidden by Khartoum to attend.

"None of the armed groups led by people like (militia leaders) Gabriel Tanginya and Paulino Matib and others collectively known as the Southern Sudanese Defence Forces (SSDF) came for this conference", Pagan Amum, a member of the SPLA/M leadership council, told Reuters.

The government, which also had delegates at the meeting, said the militia leaders, most of whom also hold positions in the Sudanese Army, had decided to skip the conference because they preferred to meet SPLM/A leader John Garang separately.

"They have not been denied permission to travel, but they prefer direct dialogue with the SPLA. They say they are not political organisations," said Ali Tamin Fartak, Sudan's minister for aviation, who is also the head of the ruling National Congress Party's southern department.

Garang said earlier in the week he was hoping to speak with the militia leaders separately.

"Participants called on the SPLM/A to enter into immediate dialogue with the armed groups with a view to integrate them as part of the territorial army of southern Sudan," said a statement by the Moi Africa Institute, the meeting's organisers, suggesting a move to bind the militias to the peace deal.