Capital gain ( sale is more but registery is less )

Dear Experts One of my known has sold agriculture land situated in rural area ( beyond municipality limit) for Rs.55 Lacs in cash and entire cash is deposited in bank in 2011.Registration is done with 36 Lacs only. He again purchased the agriculture land for Rs.34 Lacs and with rest of the amount squared of his debts and nothing invested. He received now income tax notice. My question is that can capital gain or other risk can be there as it is rural agriculture land and only confusion is difference between sale price and registration value.