Disallowance U/s 40A(3) for travelling expenses

Suppose an Organization paid travel advance to its employee say Rs. 60,000/- via NEFT as travel advance. The said employee after completing the tour submitted his claim statement for an amount of Rs. 59,000/-. While checking his tour claim statement it has found that he has incurred the expenses majorly in cash and even paid hotel bill etc to a single hotel exceeding Rs. 10,000/- a day for multiple rooms to accommodate the other officials. So, in such a case does 40A(3) apply to the Organisation who paid the tour advance via NEFT to its employee?