The Rt Rev John Pritchard outlined his concerns in a letter to the Secretary of State for Education Michael Gove.
He sought reassurances that proposals to change GCSEs more generally will still allow students from poorer backgrounds to flourish.
The bishop said the "debacle" over GCSE English grades was a "considerable affront to natural justice".
"Efforts to raise the aspirations of pupils from less favoured backgrounds are not made any easier," he said. "I would very much like to hear how the changes you propose to GCSE examinations will enable students from the same demographic to achieve and move on to the next stage of their education.”
Philip Mantell, director of education for Exeter Diocese, said church schools across the diocese had been hit and particularly two Church of England schools serving deprived communities.
At All Saints Academy, in Plymouth, A*-C grades in English were down 12% on what they expected, affecting 22 pupils.
At St Cuthbert Mayne, in Torbay, A*-C grades in English were down 10% points on what they expected, with 20 pupils affected.
The Rev Jan Ainsworth the Church of England’s chief education officer said: “We recognise that grade boundaries are adjusted during the process but the shift in the English C/D boundary was exceptional. It has disproportionately affected those children who have had to overcome greater difficulties in reaching the top grades. We are amazed at the loss of talent that has been the result.”