Other extra costs included more time spent by staff on the road, visiting different sites, or patients in the community, meaning less “productive” hours.
And it said previous research had found that those in rural areas tended to be sicker by the time they used health care services, perhaps because access was more difficult.
As a result, diseases such as cancer were diagnosed later, when treatment is more expensive, and less likely to be successful, such studies found.
Rural populations are older, with 24 per cent of the population being over 65, compared with 16 per cent in urban areas, data from the Department for Environment, Food and Rural Affairs shows.
The factors used to decide how funding is allocated take at least £1.3 billion a year away from rural areas, the study found.
Professor John Appleby, the Nuffield Trust’s chief economist and director of research, said: “The evidence is mounting that small and remote hospitals face higher costs that they cannot avoid, with comparatively poor performance against key NHS measures and dire financial positions.
“It is certainly worrying that the methods used to allocate funding to these hospitals are inconsistent, obscure and depend so heavily on judgment. We recommend that the true scale of costs is examined again, and that national bodies are much clearer about how they make their funding decisions.”
Jan Sobieraj, chief executive of the National Centre for Rural Health and Care, said: “This report is showing us that there is growing evidence that rural healthcare is not properly funded.”
“The choice that trusts in these areas have is to either have a deficit, or find themselves in danger of not having enough resources to cover the service.”
The report said efforts to adjust funding to recognise unavoidable differences in the cost of land, buildings and labour have been in place since the early 1980’s but tended to work to the advantage of urban areas.
And it said attempts to give small uplifts to some remote areas had been allocated in an “arbitrary manner” leaving some with nothing extra.
Analyists said changes in the funding formulas would leave rural areas disproportionally worse off from April, with hopes that some improvements could be seen from 2020.
An NHS England spokesman said: “People in every part of the country will benefit from NHS funding rising by at least 17 per cent over the next five years, as part of investment worth £570 billion to support the long term plan for the health service.
“The NHS funding formula is overseen by an independent panel, and already accounts for unavoidable costs related to providing services in rural areas, and we will continue to work with local hospitals and health groups to ensure that the formula is based on the best possible evidence of the needs of different communities.”