The upper limits on fares remain unchanged.
The move is aimed at helping the airlines amid a devastating second wave of COVID-19 which has reduced air travel significantly.
India had imposed lower and upper limits on airfares based on flight duration when services were resumed on May 25 last year after a two-month lockdown.
On Friday, the official order said the lower limit for flights under 40 minutes of duration will be increased from Rs 2,300 to Rs 2,600 — an increase of 13 per cent.
Similarly, flights with duration between 40 minutes and 60 minutes will have a lower limit of Rs 3,300 instead of Rs 2,900 now, the order said.