Section 40A(3) of the Income Tax Act, 1961 reads as follows
"Where the assessee incurs any expenditure in respect of which a payment or aggregate of payments made to a person in a day, otherwise than by an account payee cheque drawn on a bank or account payee bank draft, exceeds twenty thousand rupees, no deduction shall be allowed in respect of such expenditure".
Hence provisions of section 40A(3) applies to all the expenditure except those which are laid down in Rule-6 DD.
In your case:
1) Loans/Advance to staff if repayable will not come under the scope of this section as this is not an expenditure which can be claimed u/s 30 to 37 as a charge against profit, hence provisions of section 40A(3) will not be applicable.
2)Advance for expense to be incurred (for giving advances to branch) will not also come under the scope of this section as here only transfer of funds are taking place but actual expenditure is not happening, hence provisions of section 40A(3) will also not be applicable.
In all other cases, will be applicable, as such.
CMA. BK Harichandan.