The committee of the Federal Investigation Agency, headed by Mohammad Ghalib Bandesha, recorded Khan's statement.
Gen Mirza Aslam Beg, who was the army chief at the time, and Lt Gen (retired) Asad Durrani, who headed the Inter-Services Intelligence agency, are likely to be called by the committee, Dawn News quoted its sources as saying.
The former chief of Mehran bank, Younus Habib, who arranged the funds distributed by intelligence agencies, too would be called during the probe.
The panel has been asked to complete its investigation in six months.
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The Supreme Court had on October 19 ordered legal proceedings against Durrani and Beg for their role in the affair.
In a petition filed in the apex court in 1996, Asghar Khan accused the ISI of financing several politicians ahead of the 1990 polls to create the Islami Jamhoori Ittehad and to prevent Benazir Bhutto's Pakistan People's Party from winning.