MSF was angered by the probe into the deaths of five staff
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British aid agencies say they are staying in Afghanistan, despite the worsening security situation in the country.
French agency Medecins Sans Frontieres announced on Wednesday it would pull out of Afghanistan after 24 years.
It had been feared the group's departure could prompt other agencies to follow it out.
British agencies said they were surprised at the move, but had no plans to leave.
Most British agencies have their foreign staff based in the capital Kabul, with projects in provincial areas staffed by local workers.
MSF said it was withdrawing because it was unhappy at a government probe into the deaths of five of its staff in June.
It accused US-led forces of using humanitarian aid for "military and political motives", a claim the US rejected.
Morale blow
Paul Barker, director of the Afghanistan operation of CARE International, said MSF had been a significant presence in the country.
"It affected morale. A lot of us were surprised as MSF has a reputation for working through difficult times," he told BBC News Online from Kabul.
He said security threats in Afghanistan had become more frequent in recent weeks.
"It's summer fighting season, after the opium harvest when it is all being transported. [But] most of the violence is aimed at the election process; in one two-week period the UN lost 12 vehicles," he said.
"There were a number of unexploded devices found in Kabul today, that blocks the road for hours. A couple of rockets landed at night, there are periodic warnings of kidnappings and curfews in most cities.
"There's a heightened anxiety."
Oxfam, the British Red Cross and the Department for International Development also said their staff would stay in Afghanistan, although security would continue to be monitored.
Resentment
Siddo Deva, from Oxfam, said foreign aid workers were taking stringent precautions.
"They move from their offices to their guesthouses with their windows shut. They rarely go out to restaurants or shops. It's a difficult life but it's also very dull," he said.
He said the number of foreign staff in the capital was breeding resentment among the local population.
Mr Deva, who was in Afghanistan in May, said agencies need more Afghanis employed as managers. One government minister had even told him there were "too many white faces".
He said the targeting of MSF workers and the group's subsequent withdrawal should provide a wake-up call to all aid agencies.
"We have to look at whether we are changing the lives of Afghanistan's people in tangible ways or are we too worried about security," he said.
He said while protecting staff was important, "if you are going to be locked up in your guesthouse then what is the point of going?"