Frist there is no set principle for charging the fee for incorporating any company,whether the comapny is pvt or ltd or section 25.An incorporation cost vary from professional to professional.It is advisable that you should research on this.In so far as the statutury fee,please find below the fee structure ,if the section 25 company is having 5 lacs:
MOA INR 16,000
AOA INR 300
For filing the E-form 24A fee for lincese charged is INR 500.
There is no stamp duty charge applicable on the Section 25 comapny.
Hope this info may be useful for you.