Yes, if Pvt Ltd co issue shares at premium and that amount is so exceeded above its FMV of shares then excess amount received by Pvt Ltd co. over it's market value shall be taxable under section 56(2)(viib).
For ex: If FMV of shares of XYZ Pvt Ltd. are Rs. 25 (Face value Rs. 10) but the Company issue shares at Rs. 95 per share then excess amount i.e. 95-25 = 70 shall be taxable in hands of XYZ Pvt Ltd. u/s 56(2)(viib).