* Foreign Minister Kutesa says troops in S.Sudan will pull back after deal
* Uganda to send 400-strong contingent to Central African Republic
* Kutesa says anti-gay law not intended to be "witch hunt"
By John Irish
PARIS, May 9 (Reuters) - Uganda said on Friday it was worried that warlord Joseph Kony could take advantage of conflicts in the region, and promised to pull back its troops in South Sudan once a U.N.-led mission was at full strength, to focus on pursuing Kony's Lord's Resistance Army.
Uganda sent forces into South Sudan to back the government shortly after fighting broke out in December between soldiers loyal to President Salva Kiir and to his sacked deputy Riek Machar. Months of peace talks have produced little result, although Kiir and Machar were reported to have agreed a ceasesire on Friday night, in their first face-to-face meeting since the conflict began.
Uganda's deployment raised alarm among some regional neighbours and Western capitals, who feared it could escalate the clashes into a regional conflict.
"As soon as the regional force working with the United Nations is in place, Uganda will withdraw and only stay in South Sudan to fight the Lord's Resistance Army, which is what we were doing prior to this conflict," Foreign Minister Sam Kutesa told Reuters in an interview in Paris.
The U.N. mission in South Sudan, known as UNMISS, has approximately 8,500 military peacekeepers and police, and is due to be increased by another 4,000.
Kony, who has been indicted for war crimes by the International Criminal Court in The Hague, waged a brutal guerrilla war against the Ugandan government in the north of the country for nearly two decades, before fleeing with his fighters into the jungles of central Africa around 2005.
HUNTING FOR KONY
The United Nations said on Tuesday that Kony and some of his commanders were hiding in Sudanese-controlled areas of a disputed enclave in South Sudan bordering both Sudan and the Central African Republic.
A 5,000-strong African Union Regional Task Force - supported by 100 U.S. Special Forces commandos - has already been hunting Kony and his commanders, who are accused of abducting thousands of children for use as fighters in a rebel army that earned a reputation for chopping off limbs as a form of discipline.
"His forces' capacity to wage war has been greatly diminished," Kutesa said. "They are now in small groups, but we think it is important we finish this matter because the kind of conflict in South Sudan will give him a shot in the arm."
Kutesa attended talks this month with U.S. Secretary of State John Kerry and foreign ministers from neighbouring Ethiopia and Kenya to try to help put an end to the increasingly tribal-based killing in South Sudan.
asked whether a transitional government in South Sudan should include Machar, he said there should be an inclusive government with "room for his people", but that the priority was the agenda of the new government.
"South Sudan needs reforms. Institutions need to be built and the pillars of state need to be put in place," Kutesa said. "I hope that this (deal) doesn't rush them into an election as it doesn't solve anything."
"NO DISCRIMINATION AGAINST GAYS"
Kutesa said Uganda had also agreed to send 400 troops to Central African Republic to help stop a conflict between Muslims and Christians in which thousands of civilians have died.
Ahead of visits to China, Russia and the United States, the 65-year old Kutesa, who has been in his post since 2005, was in Paris to outline his priorities before taking over the presidency of the U.N. General Assembly later this year.
Uganda has come under criticism from Western nations since President Yoweri Museveni signed a law in February that toughened existing rules against gays and prescribed life in jail for what it called "aggravated homosexuality".
Kutesa said this did not amount to discrimination.
"One thing we cannot tolerate is discrimination because of someone's sexual orientation," he said. "We will not allow a witch hunt, or anybody taking it into their own hands," he said.
Critics says Museveni, who has ruled Uganda since 1986 and is widely expected to seek another term in 2016, may have been prompted to back the legal crackdown on gays in part to shore up his own support.
Uganda now has some of the toughest anti-gay laws on a continent where 37 states ban homosexuality.
"What we are concerned about is promotion," Kutesa said. "If this is your private idea, let it be yours. You don't have to promote it. This is our main objection." (Reporting By John Irish; Editing by Kevin Liffey)