This is due to a concept called expense ratios. 

The expense ratio is defined as the annual fee that an investor is charged for the management of his or her funds.

For example, if you’re investing Rs 10,000 in a fund with an expense ratio of 1.5%, then you are paying the Mutual fund Rs 150 a year to manage your money.

The NAV is a deduction of a fund’s expense ratio. Hence, the higher the expense ratio, the higher is the deduction and the lower is the NAV. The expense ratio in Regular funds is higher as compared to Direct funds, which means that the NAV in Regular Funds is lower than in Direct Funds.