Last week, Michael V Bhatia became a casualty of the US Army's "human terrain" programme. Studying for a political science doctorate at Oxford, he was serving as a civilian with the 82nd Airborne Division when he was killed by a roadside bomb in Afghanistan.

Faced with the long conflict there and in Iraq, the US military has realised that sheer firepower is not enough. The Pentagon has discovered the "human terrain" or what General David Petraeus calls the "cultural terrain" and has been recruiting anthropologists and social scientists to map it and advise commanders on local social networks.

Despite an outcry from critics, academics have been joining the Defense Department's "human terrain system" (HTS) teams out of a sense of patriotism or for the reputedly high salaries on offer. Bhatia himself is reported to have strongly defended the programme. The HTS, according to the military, is "designed to address cultural awareness shortcomings by giving brigade commanders an organic capability to help understand and deal with 'human terrain' - the social, ethnographic, cultural, economic and political elements of the people among whom a force is operating".

The Bush administration is just trying to buy more time, says John Kelly, chair of the University of Chicago's high-ranked anthropology department and joint organiser of a conference on anthropology and global counterinsurgency held there last month. Objections to the HTS programme range from the inherent secrecy of mission-oriented research to, as eminent anthropologist Marshall Sahlins observes, "manipulating local culture, imposing [our government's objectives] on them, transforming anthropologists into spies, and putting people you work with [in the locale] at risk". Last November, the executive board of the American Anthropological Association (AAA) formally discouraged its members from taking part in HTS programmes.

Hugh Gusterson, of George Mason University, Washington and David Price, of St Martin's University, Virginia formed the Network of Concerned Anthropologists to urge colleagues to pledge "non-participation in counter-insurgency". Over 1,000 anthropologists in the past six months have signed the pledge.

Proponents of the HTS programme, such as anthropologist Montgomery McFate, a senior adviser to the HTS system, argue that savvy, integrated systems yield humane and streamlined combat operations. "The ultimate goal," Sahlins retorts, is merely "better aim" - more pinpointed killing. "They call it humane because they want to target people better."

Others fear the more insidious distortion of scholarship by Pentagon money. "The HTS teams are, in some ways, the easy case," says Gusterson. "The hard case is the constant, slow, military infusion of resources into the academy." There are several examples. The Minerva Consortia Project is a Pentagon-funded incentive for universities to promote research on certain areas of interest to the military. The National Research Council advised the Pentagon to double its research budget for behavioural and social sciences, in order to ådevise "important specific applications addressed to military needs".

HTS advocates declined invitations to the Chicago conference, but scholars such as Brian Selmeski, at Air University, Alabama, and Kerry Fosher, of Marine Corps Intelligence Activity showed up to make spirited cases for "working within the system".

The conference also dissected the Counterinsurgency Manual, a military document that became a US bestseller. The manual implies "an endless future of counterinsurgency interventions," Kelly notes. "It contains no section on withdrawal." Given that the one thing scholars-for-hire cannot say is that the mission abroad is a bad idea, how can they really be scholars? What is the point of helping the government "perform a bad mission better"? someone asked.

What should anthropologists do to help? The AAA says anthropologists are "obliged to help improve US government policies through the widest possible circulation of anthropological understanding in the public sphere".

"Anthropology works best when it is in conversation," said Kelly, who praised the military participants at the conference for their candour and courage. "We have to discuss and do real research and find things we don't already know."

· This article was amended on Friday May 16 2008. Brian Selmeski, not Selmanski, is an anthropologist at Air University, Alabama. This has been corrected.