The ministry followed the IPC in suspending PCI in the wake of "poor" management of the National Para Athletics Championships in Ghaziabad last month.
"We expected the sports ministry to take such an action after our international body IPC suspended us. At our AGM on 17th of next month, we will decide who is going to be the next president and how the international suspension can be lifted o that our athletes can compete in international tournaments," Nandkishor said.
In the meantime, the blame game between suspended president Rajesh Tomar and other office-bearers has intensified with PCI levelling more allegations against him for abuse of his chair including serious financial irregularities.
The fresh infighting within the association has put the future of the athletes into further uncertainty. Though the sports ministry wants IPC to form an ad-hoc committee for the smooth running of PCI, it remains to be seen how much time it takes before its international suspension is lifted.
The athletes are in danger of missing the qualifiers for the Rio Paralympic Games beginning July and World Championships in Doha in October.
"We will request the IPC to let our athletes compete until the suspension is revoked," added Nandkishor.
Tomar, the suspended chief, remained unreachable for comments.
The IPC has suspended PCI indefinitely for the third time.