But he said the Taliban would not succeed in driving the UN out of Afghanistan, in the same way it was forced from Iraq six years ago after a suicide truck bombing on a UN compound killed a top envoy and more than 20 others.
"We will certainly continue our work, but we are taking the measures in order to do so and we are enhancing our security," said Mr Eide.
Meanwhile, British forces are continuing to hunt the Afghan policeman who shot dead five UK soldiers on Tuesday in Helmand.
They are investigating whether the gunman - who opened fire in a compound where the UK troops had been mentoring Afghan police - is linked to the Taliban.
In the guesthouse raid last week, UN employees tried to flee as three heavily armed Taliban militants hiding explosive vests under police uniforms attacked.
THE UN IN AFGHANISTAN
The United Nations Assistance Mission in Afghanistan (Unama) - set up in 2002 - is the umbrella body for all UN agencies
Role is to promote peace and stability in Afghanistan focusing on humanitarian and political issues
Most UN agencies have a major presence in Afghanistan
Major areas of activity include reconstruction, food distribution, political outreach and elections
UN employs about 5,600 staff across Afghanistan
UN also works in partnership with hundreds of governmental and non-governmental organisations
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