Two-thirds of Irish charities have taken steps to increase transparency and strengthen governance over the last six months.
But a national conference on the charity sector organised by Wheels, which represents 950 charities, was told that negative publicity surrounding the Central Remedial Clinic (CRC) and Rehab Group is still damaging the sector.
Rehab Group chief executive Angela Kerins stepped down last month following controversy over her €234,000 salary and other issues.
And last December CRC chief Brian Conlan resigned following the controversy over top-up payments at the organisation.
Wheels revealed that a survey of 297 charities conducted in April found that 61pc said their fundraising had been affected while 47pc said that funding had fallen by up to 10pc.
But the conference, attended by 200 charities in Croke Park, also heard that a significant number of charities had taken steps to improve transparency and governance.
These steps included publishing annual accounts online, publishing senior staff remuneration details and adopting a code of practice for community, voluntary and charitable organisations.