Income tax implications on land purchase at more than guideline value by a charitable trust

Land purchased by a charitable trust at a value higher than Guideline value (Market value is higher than guideline value). Registered with stamp for the value in the deed . Now The Income tax (exemptions) Dept propose to disallow the apllication above guideline value and tax on amount paid higher than guideline value. All payment made to the seller and seller filed return of income with capital gain . Purchase at higher value is a genuine transaction .Please advise.