Khatun, who won a bronze in powerlifting in the women's lightweight (up to 61kg) category in the 2014 Commonwealth Games, has also written a letter to Prime Minister Narendra Modi seeking his intervention for her selection in the Indian team.
The IOA has written a letter to the Commonwealth Games Federation to resolve the issue so that Khatun can participate in the multi-sporting event.
In the letter addressed to the Chief Executive Officer of the Commonwealth Games Federation, IOA Secretary General Rajeev Mehta has pointed out that Khatun has qualified for the Gold Coast CWG according to qualification norms and the parent international body has also confirmed this.
"The omission of Ms Khatun was taken up by the Paralympic Committee of India with the IPC. The IPC confirm that she is eligible for qualification. So, the IOA seeks your assistance with regard to Ms Khatun's qualification in 2018 Gold Coast Commonwealth Games.
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"We sincerely hope it is only a clerical error and there is someway for us to resolve qualification issue and sports entry at the earliest."
Mehta told PTI that a reply from the CGF is awaited but he hoped that the issue will be resolved so that Khatun can take part in the 2018 CWG.
"We could not have done anything different. The CGF sent us the qualified Indian athletes by name and it must have been done after consultation with the International Paralympic Committee (IPC). So, we sent it back by confirming it," he said.
PCI vice-president Gursharan Singh said the confusion was also in part due to the new quota system under which the CWG organisers have fixed how many athletes a country can send in a particular event.
"Now, the CWG participation is through quota system. The organisers will fix the number of players a country will send in a particular event. In case of para sports, the IPC will decide who qualifies or not according to the rankings.
"We have written a letter to the IOA as well as our parent body IPC and we are hoping the issue will be resolved. Ms Khatun deserves to be in the 2018 CWG and I hope she will be there.