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KABUL, Afghanistan — Defense Secretary Robert M. Gates said Monday that the United States was “well positioned” to begin withdrawing some U.S. troops from Afghanistan in July, but he said that a substantial force would remain and that the United States was starting talks with the Afghans about keeping a security presence in the country beyond 2014.

At a joint news conference in the Afghan capital with President Hamid Karzai, Gates said that no decisions had been made about the number of troops to go home. His remarks were tempered with enough caveats, however, to suggest that the July drawdown promised by President Barack Obama could be minor.

“As I have said time and again, we are not leaving Afghanistan this summer,” Gates said.

Currently about 100,000 American troops are in the country.

Gates also used the news conference to offer an extended apology to Karzai for the mistaken killings last week of nine Afghan boys. Karzai accepted the apology.

On Sunday Karzai had rejected an apology for the killings from Gen. David H. Petraeus, the top U.S. commander in Afghanistan.

“This breaks our heart,” Gates said as he stood beside Karzai in the Afghan presidential palace. “Not only is their loss a tragedy for their families, it is a setback for our relationship with the Afghan people.”

One boy who was wounded but survived described a helicopter gunship that hunted down the children as they gathered wood outside their village. The gunners apparently mistook the children for insurgents who, hours earlier, had fired on a U.S. base. The boys were 9 to 15 years old.

Karzai, after responding that civilian casualties were at the heart of tensions between the United States and Afghanistan, said of Gates that “I trust him fully when he says he’s sorry.”

Gates, who was on an unannounced two-day trip to Afghanistan, spoke more positively than he had in recent months about what he cited as progress in the nearly decade-old war.

“The gains we are seeing across the country are significant,” he said, citing improvements in security in Helmand and Kandahar provinces in the south, as well as some progress on Afghanistan’s eastern border with Pakistan.

Gates made similar remarks to U.S. troops at Bagram Air Base earlier in the day, when he told them that “you’re having success, there’s just no question about it.”

Despite the optimism in Gates’ remarks, U.S. commanders in the east and north have seen continued violence in 2011 and two of the most lethal suicide bomb attacks in nearly two years occurred in the last four weeks. One in the eastern city of Jalalabad killed 40 people and another in Kunduz province in the north killed 32.

As for a U.S. military presence in Afghanistan beyond 2014, Gates said a U.S. team would be in Kabul next week to begin negotiations on what he called a security partnership, which he predicted would require a “small fraction” of the U.S. forces in Afghanistan today.