Gates met Afghan President Hamid Karzai on an unannounced trip to Kabul and repeated Washington's apology for the killing of the boys last week by NATO helicopters, which has increased strain on an already testy relationship with Afghan leaders.
"Not only is their loss a tragedy for their families, it is a setback for our relationship with the Afghan people," Gates told a media conference with Karzai.
Karzai complained angrily on the eve of Gates's visit, rejecting an earlier and surprisingly candid apology by US Gen. David Petraeus, commander of the NATO-led International Security Assistance Force (ISAF).
Civilian casualties were the greatest strain on relations with Washington, the Afghan leader said. International concern has also grown and the fallout from recent incidents threatens to hamper peace and reconciliation efforts.
Karzai will soon unveil a timetable for the start of a handover of security responsibility from foreign forces to Afghans. The process is to begin gradually in July, with all foreign combat forces to be gone by 2014.
Gates is expected to visit parts of southern and eastern Afghanistan where NATO commanders say they have weakened the Taleban and created "bubbles" of security they hope to link up.
Such recent successes meant they should be able to meet US President Barack Obama's July pledge, he said.
"While no decisions on numbers have been made, in my view we will be well-positioned to begin drawing down some US and coalition forces this July even as we redeploy others to different areas of the country," Gates said.
US and NATO leaders agreed to Karzai's ambitious timeline for foreign combat troops to leave, and Karzai will announce on March 21 where and when the transition will begin.
But civilian casualties have clouded the relationship and diverted attention from transition plans after a spate of recent incidents.
Analysts said making strong statements over civilian casualties allowed Karzai to rally public support, but would have little long-term effect because his relations with Washington were already so badly strained.
"That being said, there is legitimate and growing anger within Afghanistan over ISAF-caused deaths," said Joshua Foust, a fellow at the American Security Project.
The nine boys were killed while collecting firewood in volatile Kunar province. Karzai said on Sunday apologies were "not enough" and that civilian casualties caused by foreign troops were no longer acceptable.
There have been at least four similar incidents, mainly in the east, in the past three weeks.
Obama has also expressed his deep regret. UN figures show that insurgents are responsible for three-quarters of civilian casualties, although it is those caused by foreign forces that rile ordinary Afghans the most.
