First let's understand what is sec 269ST :-
With effective from 1st April, 2017, no person shall receive an amount of Rs 2 Lakh or more;
(A) in aggregate from a person in a day (or)
(B) in respect of a single transaction (or)
(C) in respect of transactions relating to one event or occasion from a person.
Kindly note that Penalty u/s 271DA will be imposed on a person who receives a sum of Rs 2 Lakh and above in cash. The extent of penalty will be a sum equal to the amount of such receipt. The said penalty shall however not be levied if the person proves that there were good and sufficient reasons for such contravention.
section 269ST is applicable only to the person who is receiving the amount and not applicable to the payer. if you are paying salary to employee than 269ST will be applicable to employee since he/she is receiving amount of 200,000 or more and penalty will be levied on employee for receiving 200,000 or more by way of other than a/c payee cheque...etc
and section 40A(3) disallow the expense if paid more than 10000 in a single day to any person.
hope above explaination clarifies your doubt...