"The decision on flight restrictions are in place until May 14," Health Minister Hridayesh Tripathi told the Kathmandu Post newspaper.
"However, charter flights will be allowed."
According to statistics of Kathmandu's Tribhuvan International Airport, domestic airlines saw an all-time one-day record of passenger numbers of 15,263 on April 28, a day before the prohibitory orders came into force enforced in Kathmandu Valley, as people scrambled to leave the capital city.
Passenger numbers, however, started to drop gradually and stood at 7,225 on Sunday.
Bus services have been halted since April 29.
Nepal has also made quarantine mandatory for everyone arriving in the country.
Foreigners flying into the Kathmandu Valley are subject to a mandatory 10-day quarantine in hotels upon arrival.
A negative polymerase chain reaction test result obtained within 72 hours prior to departure from the country of origin is required for entry into Nepal.
The Nepal government's decision came after the country's Health Ministry on Sunday confirmed infections for 7,211 people, a new daily record in infections since the pandemic hit the Himalayan country early last year.
Nepal witnessed less than 100 cases for most of the days in March but saw continuous rise of cases since April with over 7,000 cases reported on Sunday for the first time.
Nepal has so far reported a total of 336,030 confirmed coronavirus cases and 3,325 deaths.