Dear Suryanarayana,
In the absence of proper description, as to what type of defects of the defence have been pointed out by the E.O./I.O., i.e., whether in agreement or conflicting with the P.O's contentions or whether with reference to the evidence adduced during the enquiry proceedings or not, your query is merely of an academic nature that can attract varied and conflicting answers from the readers/ experts.
However, since the P.O's report is provided to the charged official well before submission of the defence brief, it is for the charged officer to scuttle down the charge/ charges or the contentions of the P.O., as based on the evidence adduced during the inquiry proceedings. Both the submissions of the P.O.as well as the Defence are, more or less, independent in nature just in aid of making view points of the E.O. crystal clear on the case. However, the Defence is free to take the adverse points of contentions of the P.O. to refute them by bringing forth the facts of the case through his defence brief to help the E.O. not to get biased with the contentions of the P.O.
In fact, the evidence adduced during the enquiry proceedings is sacrosanct for the findings of the Enquiry Officer, rather than the contentions of the P.O. The Defence is provided an opportunity to give its own observations on the contentions of the P.O. If the Defence is silent on the contentions of the P.O. the enquiry officer is supposed to analyse the evidence adduced during the inquiry proceedings vis-a-vis the submissions of the Defence, provided the submissions of the Defence are charge specific, not raising undue and uncalled for extraneous issues. So, he is free to give his observations on the submissions of the Defence with reference to the analysis of the evidence and his findings out of such evidence. He is free to leave aside the contentions of the P.O. without any comment, if those are in conformity of the allegations leveled through the Articles of Charge.
However, the E.O. does not enjoy any right to give his findings on the basis of his own knowledge or assumptions, other than the evidence adduced during the inquiry proceedings. If he does so or leave some vital points of the evidence adduced during the inquiry, only then he can be labeled with bias or prejudice.
So, if you are really facing any such problem, you must come forward with appropriate description of the case.