Mihin's Dubai-Colombo run is via Kuwait.
After losing billions of rupees since its start and after briefly halting operations, Mihin Lanka is now being operated with shared services from SriLankan Airlines, the island's national career.
Flydubai's is kicking off this month offering a one-way ticket from Dubai to Colombo at 13,000 rupees, almost 3,000 rupees cheaper than Mihin Lanka.
The Mid-east no frills carrier operates nine aircraft including Boeing 737-800NG (next generation).
Flydubai started with flights to Beirut, Lebanon on June 01, 2008, and now flies to 21 destinations in the Middle East, North Africa and Eastern Europe, the airline said.
In 12 months Flydubai has flown over 750,000 passengers, the media released said.
Mihin Lanka now it its third year operates a single Airbus A320-200 aircraft to five destinations in India catering mainly to Buddhist pilgrims and migrant workers in Kuwait and Dubai.
"Mihin Lanka's biggest selling point was its price," a senior aviation executive who did not want to be named due to the political sensitivity of issue said.
"With Flydubai offering cheaper seats flying directly to Dubai it is going to be a major blow to Mihin's (Lanka) business.