An apparent raid into Pakistani territory by US forces stationed in Afghanistan has prompted angry denunciations from Pakistani officials and renewed questions about the future of the war against the Taliban in the region.

The raid, which took place Wednesday morning in the turbulent Waziristan region, may have killed as many as 20 civilians, according to witnesses and Pakistani officials.

After months in which US military officials have expressed concerns about the Pakistani government’s willingness to crack down on Taliban militants operating in its tribal areas, news of the raid has caused speculation about whether the US is planning to take on a more aggressive role in targeting militants in Pakistani territory, and worries about what such a step would mean for the volatile US-Pakistan relationship.

According to sources in the Pakistani military and civilian government, the raid began around 3 a.m. Wednesday morning, when three helicopters carrying US and Afghan troops flew into the Waziristan village of Jala Khel.

Some troops then disembarked, witnesses say, and opened fire upon villagers.

The New York Times reported that the soldiers involved were US Special Operations forces operating outside of the normal NATO chain of command.

According to Owais Ahmed Ghani, the governor of the Northwest Frontier Province, over 20 people were killed in the raid. Ghani condemned the action as a "direct assault on Pakistan’s sovereignty" and called for retaliation.

Other Pakistani officials were also quick to condemn the raid. Nadeem Kiani, spokesman for the Pakistani embassy in Washington, told Reuters that the US forces were acting on faulty intelligence that had not been shared with Pakistan, and that those killed were unarmed civilians rather than militants.

US and NATO spokesmen in Afghanistan, as well as a spokesman at US Central Command (CENTCOM) in Florida, declined to comment. But US officials did anonymously confirm that the raid had occurred, with one official telling the New York Times that at least one child had been killed.

The raid came after a long period of friction between US military officials and their Pakistani counterparts, as the US has chafed at Pakistan’s apparent reluctance to rein in the Taliban.

Since the US-led invasion of Afghanistan in 2001 overthrew that country’s Taliban government, the Taliban, al-Qaeda, and other militants have found sanctuary in Pakistan’s Federally Administered Tribal Areas (FATA) bordering Afghanistan, in which the central government exercises little control.

A September 2006 agreement legitimized Taliban power in the Waziristan region of the FATA, and militants have used the region as a staging post for attacks into Afghanistan.

US worries only increased following the resignation in August of Pakistani President Pervez Musharraf, considered by Washington to be a key ally in the war on terror. Elections to choose Musharraf’s successor will be held Sep. 6, but US officials appear to have considerably less confidence in Asif Ali Zardari of the Pakistan People’s Party (PPP), who is the heavy favorite in the elections.

Questions also swirl about whether Pakistan’s incoming civilian government will be able to exert control over the military, which has traditionally been highly autonomous, and the country’s powerful Inter-Services Intelligence Directorate (ISI).

In a move that appeared designed to win US confidence, the Pakistani military launched an airpower offensive against the Taliban in the Bajaur region of the tribal areas in August. The campaign has been credited with killing hundreds of Taliban, but has also displaced an estimated 200,000 civilians, according to the International Committee of the Red Cross. This past week, the government declared that it would halt the campaign during the month of Ramadan.

The Taliban retaliated for the government offensive with an Aug. 21 suicide bombing at an arms factory outside Islamabad that killed over 60 people.

This past summer, US officials have begun to confront Pakistan more openly over the militants issue. In July, a CIA official traveled to Islamabad with evidence linking the ISI to the Jul. 7 bombing of the Indian embassy in Kabul.

In late August, Adm. Mike Mullen, chairman of the US Joint Chiefs of Staff, met with Gen. Ashfaq Kayani, chief of staff of the Pakistani Army, aboard an aircraft carrier in the Indian Ocean to discuss strategies for reining in militants in the tribal areas.

Several other prominent US and NATO military officials were present at the meeting, including Gen. David Petraeus, currently the top US commander in Iraq and soon to become head of CENTCOM  the military command overseeing Pakistan and Afghanistan.

US officials told the New York Times that potential unilateral US operations within the tribal areas were not discussed at the meeting. But other officials suggested to the Times that Wednesday’s raid was not a mistake or aberration, but rather the product of a concerted decision within the US military hierarchy.

"There’s potential to see more [such operations]," one official told the Times.

On Aug. 23, the Los Angeles Times reported that top US military officials have been resistant to the idea of direct military operations in Pakistan, preferring to send trainers to work with the Pakistani military. CIA counterterrorism officials, on the other hand, have been the primary advocates of direct operations.

Wednesday’s raid, however, may signal that that dynamic has shifted, and that the military brass has been convinced of the necessity of direct military intervention.

If the raid does in fact mark the beginning of a new US policy in the tribal areas, it is expected to considerably complicate US relations with the Pakistani government.

C. Christine Fair, a South Asia specialist at the RAND Corporation, suggested that the raid did mark a policy shift, and cautioned about the potential consequences of the new strategy.

"Without integrating these attacks within a wider Pakistan strategy  which the US government does not have  we risk a serious blowback which could make things worse, not better," Fair told IPS. "Ninety percent of our logistics still move through Karachi port, so attacking Pakistani targets when we are still dependent on them makes little sense."

Bruce Riedel, a former CIA officer now at the Brookings Institution, argued last month that the US should be willing to use force against "very high value targets" in Pakistan, but cautioned against "loose talk about larger military options."

"The notion of moving NATO forces into the FATA is crazy," Riedel said at a Brookings panel. "We will only spread the cancer deeper into Pakistan…Talk about these issues is extraordinarily counterproductive. It only feeds the paranoia and conspiracy theories of the Pakistani political milieu."