It also noted the absence of an integrated system of disbursal and management of the money allocated for compensating the victims.
The Nirbhaya Fund was announced by the Centre in 2013 after the December 16, 2012 gangrape and murder case in Delhi to support initiatives of the government and the NGOs working towards protecting the dignity and ensuring the safety of women.
The apex court observed that there was a lot of confusion on the issue as three ministries - Ministry of Home Affairs, Finance Ministry and Ministry of Women and Child Development were involved in it, but they did not know what is to be done.
A bench of Justices Madan B Lokur and Deepak Gupta said though the Centre was disbursing funds to the states under the scheme, there appeared to be no system as to how and at what stage the sexual assault victims have to be compensated.
"There seems to be no system as to how funds have to be disbursed, how victims have to be compensated and at what stage the compensation has to be paid. This is an unhappy state of affairs," the bench said.
The court asked the Centre, senior lawyer Indira Jaising, an amicus curiae in the matter, and other concerned officials to give their suggestions as to how the system of granting compensation to such victims should work best and how they could be rehabilitated.
The bench fixed the matter for next hearing on October 4.
During the hearing, the court expressed its displeasure over the Centre's affidavit and pointed out several instances where state-wise details of the number of such victims and the amount of compensation given to them were not given properly.
"There must be some application of mind (before filing an affidavit)," the bench said, adding, "You cannot come and file affidavit like this in a court. You are dumping this on us."
At the outset, Indira Jaising told the court that there was no uniformity in the disbursal of funds to the victims of sexual assault as in states like Goa, the amount was Rs 10 lakh while in some other states, it was only Rs one lakh.
The counsel appearing for the Centre told the bench that they would file a better affidavit giving details of the issues raised by the court as well as the amicus.
Ms Jaising argued that the Centre was transferring Rs 200 crore under the scheme to each state which should furnish a compliance report on the amount spent and also whether the money was given to the victims or not.
However, the bench asked her to go through the rules formulated by the states and give a model set of rules which could be directed.
"We will take up the matter in October and will pass one set of directions. We will indicate that there is a lot of confusion. Three ministries are involved but they do not know what is to be done. We will pass directions," the bench said.
Six petitions were filed in the Supreme Court between 2012 and 2013 after the gangrape case in Delhi on December 16, 2012 raising concerns over the safety and security of women.
All the petitions were tagged by the apex court and several directions have been issued from time to time in this regard.
Ms Jaising had earlier told the apex court said that the Victim Compensation Scheme under section 357(A) of CrPC has not been notified by all the states.
(This story has not been edited by NDTV staff and is auto-generated from a syndicated feed.)