The funds have been lost following the closure of brain injury unit Bridgehead House that was set up by Leonard Cheshire in collaboration with health trusts in the Humberside area.
The charity blames the closure on the trusts, which referred only 15 patients to the centre since it opened 18 months ago.
The breakdown in the relationship between the charity and the NHS comes at a time when the Government wants to roll out cross-sector partnerships.
Bryan Dutton, director general at Leonard Cheshire, said: "We are saddened and extremely frustrated by this unnecessary situation. We know how much this specialist service is needed - and we cannot understand why some local health services are failing to refer people to it.
"In doing so they are denying brain-injured people their rights to the very best standards of care available. The impact on them and their families is incalculable."
The specialist centre in Goole opened in January 2002 following a fundraising campaign in the North East.
While trusts in Lincolnshire have referred some patients to the unit trusts in Hull and East Yorkshire have not transferred a single person.
The charity announced last week the unit will shut its doors in August.
Dutton said: "This issue has exposed serious shortcomings in some of the local health services' processes for assessing and referring brain-injured people.
"It seems to be something of a postcode lottery that decides whether or not the person with a serious brain injury is given the highly specialised level of care and support they need."
Claire Wood, director of nursing, quality and clinical services at East Yorkshire Primary Care Trust blamed Leonard Cheshire's inflexible admissions policy. "No transfers have been made either because the patients did not meet the admission criteria, or because the patients chose not to move.
More patients would benefit if the selection criteria for admission and programmes of care offered were more flexible," she said.
The home's closure poses a dilemma for the Treasury. In its latest review of the role of the voluntary sector in the provision of public services, health care was designated as one of five areas where involvement is set to grow.
Dutton said that Leonard Cheshire would be "very sensitive" about any future joint projects with the NHS. "Without collaborative risk sharing, the risk is too great," he said.