The petitioners had alleged in the PIL that the loans were given to shell companies.
The Ministry's affidavit further said that the remaining issues and violations reported in the inspection report are under examination and same will be dealt as per law.
"As far as the loans given by IBHFL to five companies, which are the subject matter of the instant writ petition, the report states that loans given to Amricorp, ADAG, DLF have been repaid and loans given to other two entities viz. Vatika and Chordia reported to be 'Standard Accounts'," the affidavit said.
The Ministry, however, informed the court that it is yet to receive the third inspection report, in respect to Indiabulls Real Estate Ltd (IBREL).
A PIL was reported to have been filed on September 27 that alleged the round-tripping of funds by the company.
Indiabulls Housing Finance, in a statement, said: "The facts stated in government affidavit, filed today, provides a true and clear picture about the allegations made in the PIL."