Paul Saquee, the chairman of the council of chiefs in Sierra Leone's eastern Kono region, said disruption to the long-term agricultural development projects of one NGO would have knock-on effects. "It means the work they were doing before suffers and next year we will have less food supply," he told Reuters.
In Liberia, the epidemic dashed President Ellen Johnson Sirleaf's hopes of shifting the focus of aid to investment.
"Now Ebola is here and all of those efforts have been brought to a standstill. We could be starting from scratch again," said Jennah Scott, director of the Liberia Philanthropy Secretariat, a government agency. "That is very heartbreaking."
The World Bank and other donors have pledged hundreds of millions of dollars in aid. But Scott is concerned that money will go mostly to United Nations agencies and large NGOs, rather than local organisations.
"We need to get more support to local NGOs because they are the ones who stay in Liberia," said Scott, whose organisation channels around $20 million in aid a year into Liberia.
The WaterAid organisation, which works to improve access to safe water, hygiene and sanitation services in developing countries, had to suspend plans to drill 100 boreholes in Sierra Leone and provide services to four villages in Liberia.
Apollos Nwafor, WaterAid's West Africa advocacy manager, said the countries hit by Ebola suffered from broken health systems and food insecurity as well as a lack of safe water, sanitation and hygiene.
WaterAid was now lobbying donors to step up funding in these areas. "Ebola has become a hydra-headed crisis," Nwafor said.
OneVillage Partners, a rural development agency, started seven years ago with post-war reconstruction in villages in eastern Sierra Leone. It has since moved into other activities such as micro-loans for small business.
Since the Ebola outbreak, it has used its knowledge and relationship with villagers to educate them about Ebola, even though this was not its area of expertise.
The group suspended its programmes in July and laid off some staff. Now its activities include delivering soap and working with communities to stop the spread of the disease.
While the virus has set the clock back on years of promising aid initiatives, the immediate work of showing local people how to avoid becoming infected is vitally important.
"Everywhere we looked, there was just wholesale denial and a lot of misinformation going around about Ebola," said Chad McCordic, Community Project Manager at OneVillage Partners.