Barnardo's Northern Ireland has said it is set to lose almost 1m when the funding ends.
The announcement of the ending of the Children's Fund in 2006 was made last month by the Northern Ireland Office in its Revised Priorities and Budget 2005 to 2008.
Children's Fund projects have been allocated 17m for the three years from 2003 to 2006.
Pauline Leeson, director of Children in Northern Ireland, an umbrella organisation for the voluntary childcare sector, said there was a 'financial crisis in children's services'.
Ms Leeson said that 25 staff from one project were made redundant before Christmas and three projects have been told that their funding will stop at the end of March.
She said, 'We were led to believe that if we monitored and evaluated the projects, and they proved to be valuable and effective, the funding would be secured. But we are now having to compete with health and social services, who need money for hospital beds.'
The current Children's Fund supports projects on early preventive family support for parents, children with learning disabilities, play schemes for traveller children and children at risk of re-offending.
Over the past year Barnardo's has spent 315,000 of the 1m three-year allocation on family group conferencing for children with behaviour problems, support for teenage mothers and parenting courses in deprived areas.
Lynda Wilson, director of Barnardo's Northern Ireland, said, 'We are not just alarmed by the disappearance of the Children's Fund, but disappointed that in spite of the Government's perceived commitment to children, the recent budget proposals do not adequately reflect this commitment.'
Nigel Williams, Northern Ireland Commissioner for Children and Young People, met with finance minister Ian Pearson MP last week to look at ways to mainstream the funding.
But although Mr Pearson has pledged to get in touch with the Department of Health, Social Services and Public Safety about ring-fencing the money, a spokesman for the Commissioner said there were concerns because 'all these departments are cash-strapped'.
The Commissioner has asked the finance minister to look at how funding for children's services in Northern Ireland compares to the rest of the UK.
In England, Children's Fund partnerships have been given a three-year allocation that covers them until 2008. After that, the fund is expected to be absorbed into Children's Trusts.
