Ms.Sowmya.S.,
Sec 40A(3) - Cash Payments in excess of Rs.20,000 - 100% disallowed subject to exceptions given in Rule 6DD - Obviously the disallowance is with respect to REVENUE EXPENDITURE sought to be claimed as a deduction while computing income under the head "Profits & Gains of Business or Profession".
Capital Expenditure - which cannot be claimed as a deduction u/s 30 - 37 - is outside the purview of Sec 40A(3).
Sec 269SS - Prohibits the Recepient from accepting cash greater than or equal to Rs.20,000 by way of any loan or deposit otherwise than by an account payee cheque or account payee draft. Penalty for failure to comply with the provsions of Sec 2699SS is given u/s 271D which is equal to the amount of loan or deposit accepted.
Sec 269T - Proibits repayment of any loan or deposit in cash greater than or equal to Rs.20,000. Penalty for failure to comply with the provisions of Sec 269T is given u/s 271E which is equal to the aount of loan or deposit repaid.
I hope the above clarifies your query regarding allowance/disallowance of expenditures/payments in cash.
regards
CA.P.Ramasamy