In a letter to ministers, Dr Stuart Burgess, the outgoing chairman of the Commission for Rural Communities (CRC), said more rural working people rely on state hand-outs compared to workers in urban areas – underlining the low pay culture that blights areas such as Devon and Cornwall.
The warning, issued as the commission was abolished at the end of last month, comes as the Government breaks the link between benefits and inflation, cuts housing benefit for social tenants with spare rooms and caps total benefits at £26,000 a year.
The commission, which has campaigned for more affordable homes in the countryside and rural communities to be linked up to fast broadband connections, is being replaced by a Rural Communities Policy Unit that will sit within the Department for Environment and Rural Affairs (Defra).
Along with axing the Rural Advocate role in 2010, critics say the countryside has been left without an independent voice for the first time since 1909.
In the letter to Environment Secretary Owen Paterson, Dr Burgess argues "hidden and dispersed poverty and disadvantage" exists "even in the most affluent rural areas".
Average pay in the UK is £26,664 a year – but is much lower in Somerset, where it is £23,595, Devon £22,214, Plymouth £21,978, Cornwall £20,952 and Torbay £19,509.
Dr Burgess writes: "A higher proportion of people in work in rural areas need to claim welfare benefits compared with their urban counterparts, and they will find their poverty intensified by the proposed benefit cuts.
"Indeed two-thirds of working-age people experiencing poverty in rural areas are in work. It is important that they are aware of the benefits which are available to them, and that Government takes this into account when making changes to benefit criteria."
He adds: "Child poverty is lower in rural areas, but is projected to rise, mainly as a result of the decision not to increase benefits in line with inflation."
The missive does praise the Government's Rural Statement, which promised to help revive rural communities, and welcomes pledges to "rural-proof" policies so countryside communities receive fair treatment.
But a series of "challenges" include alleged unfairness in Whitehall funding that prioritises cities. MPs have recently highlighted a "rural penalty" that sees urban authorities get 50% more cash from central Government than rural counterparts. The gap will be narrowed by just 0.2% this year.
"We hope that Government will be able to address the continued discrepancies," the letter says.
Dr Burgess repeats calls for the Government to ensure a co-ordinated approach to improving services and choices for rural youngsters by appointing a Minister for Youth Affairs.
It also voices misgivings about changes to school funding formulae, which place more emphasis on the pupil-weighted element at the cost of reducing funding for fixed costs.
"Whilst we understand that this has been done in the interests of increasing competition, we contend that competition is not such an issue in rural areas," the letter says.
The commission has asked for the Government to review the effects of the formula on small rural schools, many of which feel that their viability is being put at risk.
Other challenges highlighted by the letter include rural fuel poverty, health and social care and transport.
A Defra spokesman said: "Our ministers have a good understanding of rural communities and now talk directly to them through our Rural and Farming Networks and on Defra Rural Roadshows to get their advice and views."