Afghan commanders have refused more than a dozen times within the past two months to act on U.S. intelligence regarding high-level insurgents, arguing that night-time operations to target the men would result in civilian casualties, Afghan officials say.

The defiance highlights the shift underway in Afghanistan as Afghan commanders make use of their newfound power to veto operations proposed by their NATO counterparts.

For much of the past decade, NATO commanders have dictated most aspects of the allied war strategy, with Afghan military officers playing a far more marginal role. But with the signing of an agreement last month, Afghans have now inherited responsibility for so-called night raids — a crucial feature of the war effort.

To Afghan leaders, the decisions made by their commanders reflect growing Afghan autonomy from Western forces as NATO draws down, and prove that Afghan forces are willing to exercise more caution than foreign troops when civilian lives are at stake.

“In the last two months, 14 to 16 [night] operations have been rejected by the Afghans,” said Gen. Sher Mohammad Karimi, the top Afghan army officer. “The U.S. has said, ‘This operation better be conducted. It’s a high-value target.’ Then my people said, ‘It’s a high-value target. I agree with you. But there are so many civilian children and women [in the area].’ ”

Many of the rejected night operations are later conducted once civilians are no longer in the vicinity of the targets, Karimi said.

U.S. officials point to progress they have made in their own efforts to reduce civilian casualties, and say that while the Afghans occasionally choose not to act on American intelligence, night operations are nonetheless frequently conducted. Americans continue to provide logistical support and backup, U.S. officials say, using their aircraft to deposit Afghan soldiers at the targets.

“The Afghans are the ones who give final say on whether or not the mission gets conducted. That’s how the process works now,” said a U.S. official who spoke on the condition of anonymity to discuss a sensitive issue. “The operational tempo hasn’t been affected by this. I don’t think there’s been a night when they haven’t conducted a good number of operations.”

But the resistance to American guidance on night operations represents the clearest indication to date that Afghan military commanders are heeding a directive from President Hamid Karzai last month. Just a day after signing a 10-year bilateral agreement with the United States, Karzai said Afghan soldiers should discard questionable information provided by the U.S. military.

“If you have any doubt about an American intelligence report, do not conduct any operation based on it,” he told officials at the Interior Ministry.

The Afghan president grew even more disenchanted over the last week, when separate NATO airstrikes killed 18 civilians in Logar, Kapisa, Badghis and Helmand provinces, according to Afghan officials. The president and his advisers said the attacks raise questions about the newly minted partnership agreement.

“Karzai signed the strategic pact with the United States to avoid such incidents and if Afghans do not feel safe, the strategic partnership loses its meaning,” said a presidential statement released Monday.

In the past, such complaints would have been unlikely to affect military operations. But the transition to greater Afghan control of security has left Karzai and his military in a stronger position to stymie the American strategy.

The transition will continue in the coming months. This summer, a number of districts and provinces will be formally entrusted to Afghan security forces, the third round of regional transitions. In September, Afghans will assume responsibility for the U.S. military prison at Bagram, with about 3,000 detainees.

In the past, Western officials questioned whether Karzai’s opposition to night raids and other U.S.-led operations was politically driven — aimed at proving to his people that he was capable of resisting American demands.

Now, with more transitional milestones looming, Afghan political and military leaders say their growing responsibility has made the issue of civilian casualties even more delicate.

“Most of the people will say, ‘I don’t blame the foreigners if they kill us, but why do you kill me?’ ” Karimi said. “We have to be concerned. We have to have people on our side.”

Each time civilians are killed in either a NATO or Afghan operation, Karzai or one of his advisers calls the Defense Ministry for an explanation. Karimi said the president’s involvement in military affairs centers largely on reducing civilian casualties rather than on dictating troop levels or strategy.

NATO officials say they have greatly reduced the number of civilians killed in operations in recent years. The United Nations last year attributed 400 civilian deaths to NATO and Afghan forces, a slight decrease from 2010.

“We have significantly improved attention to detail when it comes to targeting,” a U.S. official said.

Human rights organizations say they fear that the methods and institutions developed by NATO to both track and prevent civilian casualties will not be replicated by the Afghan security forces.

“Right now, Afghan forces don’t have systems in place to prevent and respond to civilian casualties they may cause. International forces evolved their thinking over a decade, realizing they needed a civilian casualty tracking team and policies to investigate civilian harm caused by their own forces,” said Sarah Holewinski, executive director of the Campaign for Innocent Victims in Conflict. “Without those systems in place, verbal commitments from the Afghan government to not harm civilians are likely to fall flat as Afghan forces take over.”