Paper-based applications for things like subsidy payments and the registration of cattle is to be gradually phased out, with farmers being directed to register details online.
But the move has led to warnings farmers in rural areas without a good internet connection could miss out and the choice of using paper needed to remain.
It is thought internet applications for Single Farm Payments would be more accurate, easier for farmers to handle and cut costs by reducing the need for paper and postage. The registration of the birth, death and movement of cattle could also be handled increasingly online.
Defra is one of several Government departments facing massive reductions in budgets, with spending potentially to be cut by as much as 40 per cent.
A spokeswoman said: "We will publish a full road map on the issue later this year. The RPA needs to identify what customers want."
She added the issue of farmers with no or limited access to the web was being examined.
Alistair Mackinstosh, livestock chairman for the National Farmers' Union, said: "There are a lot of areas which do not have broadband or a good internet connection. We need to move with the technology but the paper option should be retained for farmers who cannot access that type of technology."