KHARTOUM, Aug 11 (Reuters) - South Sudan’s second largest armed group will cooperate fully with the new First Vice President Salva Kiir and place its forces at his disposal, its political leader, Riak Gai, said on Thursday.

Gai, who split from Kiir’s Sudan People’s Liberation Movement (SPLM) in 1991, spoke to Reuters at a swearing-in ceremony for the former rebel to become part of a coalition government designed to seal an end to more than 2 decades of civil war in the south.

"We are going to cooperate with him," Gai said. "We’ll do it in a way that commander Salva, being the man in charge of the security in the south, we will put the SSDF at his disposal," he said, referring to the armed wing of his movement, the South Sudan Defence Forces.

His comments indicated a major hurdle to the implementation of a peace deal reached in January with Sudan’s former Islamist government had been overcome.

The top U.N. envoy in Sudan, Jan Pronk, has said the first important task for Kiir, sworn in after former SPLM leader John Garang was killed in a helicopter crash 12 days earlier, was dialogue with other southern armed groups and political parties.

"We want him to command the people of the south and command all the forces," Gai added. The SSDF, led by General Paulino Matip, says it has almost 50,000 troops in the south.

Garang, the architect of the January deal which involved wealth sharing, democratic transformation and a southern referendum on secession within 6 years, died just 3 weeks after becoming first vice president of the unity government.

Gai who signed a separate peace deal with Khartoum in 1997, is now one of 3 vice presidents of the ruling National Congress Party, which dominates government and parliament.

He said Garang had been openly provocative towards the SSDF, but Kiir was more conciliatory.

"He has been known for his dedication for the cause of the people of the south and unity of the southern people and unity of the movement also," Gai said.

Matip, who began a failed dialogue with Garang before his death, welcomed Kiir on his arrival at Khartoum airport on Wednesday and stood at his side during a brief media statement.

"That was a sign also that we are ready to cooperate with Salva without condition," Gai said of Matip’s presence.

The war, which claimed more than 2 million lives mostly from famine and disease, broadly pitted the Islamist northern government against the mainly Chrsitian, animist south.

It was complicated by issues of oil, ethnicity and ideology.