Chairman of the High Speed Two (HS2) select committee Robert Syms wrote to Pickles following concerns raised by the National Farmers Union (NFU) at a committee session last month.
The NFU said that farmers who have buildings purchased by HS2 "could run into difficulties with planning authorities when trying to rebuild replacement farm houses and agricultural buildings on a different part of their land".
In his letter, Syms highlighted a case of a farming family in Staffordshire who face having to move to make way for the HS2 line.
The letter said the family wish to build elsewhere on their land, but could be prevented from doing so because of local planning policy.
The letter stated: "The local planning policy for this area means that permission to build will be granted only upon the demolition of the existing farmhouses, the policy being that there should be no net gain in accommodation".
The letter concluded: "Applying a planning policy too rigidly ignores the special circumstances arising from construction of the railway: a policy of protecting the green belt might sensibly be adjusted to allow for individual buildings to be retained where they remain useful and where the new buildings have been essentially forced on those affected as a way to maintain the area while reducing the impact of the railway".