The company had mobilised funds from the public through issuance of redeemable preference shares (RPS) and non-convertible redeemable debentures (NCDs) in 2012 and 2013 without complying with the public issue norms.
The order comes after Sebi found that Khan was director in Bharat Krishi Samridhi Industries from June 30, 2011, to March 1, 2013, when the company had decided to issue NCDs and RPS.
"The noticee (Khan) was a director in the company during the period when the decisions regarding issue of RPS and NCDs were taken and also when monies were mobilised as subscription amounts against such securities," Securities and Exchange Board of India (Sebi) said.
The regulator, in its order in October 2015, had noted that Bharat Krishi Samridhi Industries and its directors made a public issue of RPS and NCDs without complying with the public issue norms mandated under the Companies Act.
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Accordingly, Sebi ordered the firm and its directors to repay the money to investors. However, the direction was not issued against Khan.
Now, in an order passed today, the regulator said Khan "shall, jointly and severally along with the company and others as ordered vide Sebi dated October 9, 2015, forthwith refund the money collected by the company through the offer and issuance of RPS and NCDs to the investors... With an interest of 15 per cent per annum."
Minister Narendra Modi has approved Tyagi's appointment for a period not exceeding five years or till the age of 65 years, it said.
58-year-old Tyagi hails from Uttar Pradesh.
As per the eligibility criteria, a person can hold the position of Sebi chairman till the age of 65 years or for a term decided by the government.
Sinha, a 1976 batch IAS officer of Bihar cadre, had assumed office as the Sebi chairman on February 18, 2011, when the previous UPA government was in power.
He was later given a two-year extension. Days before the end of his tenure in February last year, he was given another extension till March 1, 2017.
Tyagi for a short while was also on the board of Reserve Bank of India (RBI).
The process for selecting the next chief of the Sebi started in September 2015, pursuant to which several applications were received for the position.
"Keeping in view the role and importance of Sebi as a regulator, it is desirable that persons with high integrity, eminence and reputation preferably with more than 25 years of professional experience and in the age group of 50-60 years may apply," the Finance Ministry had said while inviting applications for the post.
Sebi chairman receives consolidated pay package of Rs 4.5 lakh per month.
Besides chairman and whole-time members, the Sebi board includes independent members and nominees of Finance Ministry, Corporate Affairs Ministry and the RBI.