Every Non-Government Organisation(NGO), can apply for registration under Section 12A if it wants to get an exemption from income tax. Without the 12A certificate, the receipts of the NGO will be entitled to normal tax rates. On the other hand, a registration under section 80G of the Income Tax Act provides tax benefits (80G deduction) to all assessees who pays any sum as a donation to eligible funds or institution.
NGOs can apply for both the 12A certificate and registration under section 80G together or separately. If you wish to apply for them separately, you must apply first for 12A registration. As per the Income Tax Act, 1961, 12A registration is a must if you want to apply for registration under section 80G of the Income-tax Act.