BAGRAM AIR BASE, Afghanistan — Secretive branches of the military’s Special Operations forces have increased counterterrorism missions against some of the most lethal groups in Afghanistan and, because of their success, plan an even bigger expansion next year, according to American commanders.
The commandos, from the Army’s Delta Force and the Navy’s classified Seals units, have had success weakening the network of Sirajuddin Haqqani, the strongest Taliban warrior in eastern Afghanistan, the officers said. Mr. Haqqani’s group has used its bases in neighboring Pakistan to carry out deadly strikes in and around Kabul, the Afghan capital.
Guided by intercepted cellphone communications, the American commandos have also killed some important Taliban operatives in Marja, the most fearsome Taliban stronghold in Helmand Province in the south, the officers said. Marine commanders say they believe that there are some 1,000 fighters holed up in the town.
Although President Obama and his top aides have not publicly discussed these highly classified missions as part of the administration’s revamped strategy for Afghanistan and Pakistan, the counterterrorism operations are expected to increase, along with the deployment of 30,000 more American forces in the next year.
The increased counterterrorism operations over the past three or four months reflect growth in every part of the Afghanistan campaign, including conventional forces securing the population, other troops training and partnering with Afghan security forces, and more civilians to complement and capitalize on security gains.
American commanders in Afghanistan rely on the commando units to carry out some of the most complicated operations against militant leaders, and the missions are never publicly acknowledged. The commandos are the same elite forces that have been pursuing Osama bin Laden, captured Saddam Hussein in Iraq in 2003 and led the hunt that ended in 2006 in the death of Abu Musab al-Zarqawi, the leader in Iraq of the insurgent group Al Qaeda in Mesopotamia.
“They are extremely effective in the areas where we are focused,” said one American general in Afghanistan about the commandos, speaking on the condition of anonymity because of the classified status of the missions.
Gen. David H. Petraeus, who is in charge of the military’s Central Command, mentioned the increased focus on counterterrorism operations in testimony before the Senate Foreign Relations Committee on Dec. 9. But he spoke more obliquely about the teams actually conducting attacks against hard-core Taliban extremists, particularly those in rural areas outside the reach of population centers that conventional forces will focus on.
“We actually will be increasing our counterterrorist component of the overall strategy,” General Petraeus told lawmakers. “There’s no question you’ve got to kill or capture those bad guys that are not reconcilable. And we are intending to do that, and we will have additional national mission force elements to do that when the spring rolls around.”
Senior military officials say it is not surprising that the commandos are playing such an important role in the fight, particularly because Gen. Stanley A. McChrystal, the senior American and NATO officer in Afghanistan, led the Joint Special Operations Command for five years.
In addition to the classified American commando missions, military officials say that other NATO special operations forces have teamed up with Afghan counterparts to attack Taliban bomb-making networks and other militant cells.
About six weeks ago, allied and Afghan special operations forces killed about 150 Taliban fighters in several villages near Kunduz, in northern Afghanistan, a senior NATO military official said.
Some missions have killed Taliban fighters while searching for Pfc. Bowe R. Bergdahl, who was reported missing on June 30 in eastern Afghanistan. The Taliban in July posted a video on jihadist Web sites in which the soldier identified himself and said that he had been captured when he lagged behind on a patrol. A second video was released on Friday.
“We’ve been hitting them hard, but I want to be careful not to overstate our progress,” said the NATO official, speaking on the condition of anonymity in order to describe the operations in detail. “It has not yet been decisive.”
In Helmand, more than 10,000 Marines, as well as Afghan and British forces, are gearing up for a major confrontation in Marja early next year. Brig. Gen. Larry Nicholson, the senior Marine commander in the south, said in a recent interview, “The overt message we’re putting out is, Marja is next.”
General Nicholson said that in addition to covert operations, including stealthy commando raids against specific targets, the military was also conducting an overt propaganda campaign intended to persuade some Taliban fighters to defect.
Military officials say the commandos are mindful of General McChrystal’s directive earlier this year to take additional steps to prevent civilian casualties.
In February, before General McChrystal was named to his current position, the head of the Joint Special Operations Command, Vice Adm. William H. McRaven, ordered a halt to most commando missions in Afghanistan, reflecting a growing concern that civilian deaths caused by American firepower were jeopardizing broader goals there.
The halt, which lasted about two weeks, came after a series of nighttime raids by Special Operations troops killed women and children, and after months of mounting outrage in Afghanistan about civilians killed in air and ground attacks. The order covered all commando missions except those against the highest-ranking leaders of the Taliban and Al Qaeda, military officials said.
Across the border in Pakistan, where American commandos are not permitted to operate, the Central Intelligence Agency has stepped up its missile strikes by Predator and Reaper drones on groups like the Haqqani network.
But an official with Pakistan’s main spy agency, the Inter-Services Intelligence directorate, or I.S.I., said there had also been more than 60 joint operations involving the I.S.I. and the C.I.A. in the Federally Administered Tribal Areas and Baluchistan in the past year.
The official said the missions included “snatch and grabs” — the abduction of important militants — as well as efforts to kill leaders. These operations were based on intelligence provided by either the United States or Pakistan to be used against the Taliban and Al Qaeda, the official said.
“We can expect to see more U.S. action against Haqqani,” a senior American diplomat in Pakistan said in a recent interview.
The increasing tempo of commando operations in Afghanistan has caused some strains with other American commanders. Many of the top Special Operations forces, as well as intelligence analysts and surveillance aircraft, are being moved to Afghanistan from Iraq, as the Iraq war begins to wind down.
“It’s caused some tensions over resources,” said Lt. Gen. Charles H. Jacoby Jr., the second-ranking American commander in Iraq.
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