Can minority aided schools collect fees from students? If not who would provide them funds to run the school?

I'm the principal of Nirmala Sr. Sec. School , Port Blair, Andamans. The school was established in 1958. The school gets 95% grant from the A & N Administration towards teachers' salary only. The 5% that school manages is itself about 1Lakh rupees p.m. The school is basically to help the poor and deprived students. There are 1200 students in the school out of whom about 70% belong to adivasi communities of Jharkand and about 400 studenmts belong to BPL families. The school collects nominal fees as per Delhi Education code but since RTE is implemented the Education Department is asking us not to collect fees for classes I-VIII. All the private schools in Port Blair collect high fee but they have no problem. Since we get 95 % grant, it is said that we cannot collect fee. The maintainance of the school and the building itself is a mammoth task. Our children get free text book and free mid day meals but they do not receive free uniforms or any other facilities of the government. If we cannot collect fees then will the government fund us as the govt. schools? Kindly advise as how to go with the problem?