The concerns have arisen after the Charity Commission confirmed last week that it would publish additional guidance for charities on how to assess and minimise the risk of being compromised by terrorist activity.
Patrick Kirwan, head of internal audit at Christian Aid, said: "Our frustration may come if there are hoops to jump through that add nothing of value to our partner assessment process or prescribe courses of action that are disproportionate to the risk facing us.
"What could damage us is if our work is stymied by having to look over our shoulders and second-guess what the interpretation of our actions might be."
He added that it would be "practically impossible" to unravel links with organisations that might have connections to potential terrorist sympathisers in locations such as Sri Lanka or the Gaza Strip.
Ken Caldwell, head of international operations at Save the Children, said: "To carry out our humanitarian work, we may have to have lines of communication open with any group that is in control of a conflict zone, regardless of its affiliations."
Mohammed Kroessin, senior policy adviser at Islamic Relief, said that any extra risk-assessment obligations should be dictated by evidence.
He said: "We need to bring together a group of experts, such as people from the Overseas Development Institute and the Department for International Development, to hear their views on where the risks lie, because there is a consensus that the Home Office review has been driven by people from the security agencies."