Due to the passage of the typhoon across northern Philippines, Emirates flights EK332/333 and EK334/335 between Dubai and Manila on Tuesday have been cancelled.
Customers connecting to these flights in Dubai will not be accepted to travel at origin, the airline said in a statement, sister publication Arabian Business reported.
Typhoon Kammuri barrelled towards the Philippines on Monday, pushing tens of thousands of people into evacuation centres and prompting authorities to order a temporary closure of Manila's international airport as a safety precaution.
Kammuri was expected to make landfall late Monday or early Tuesday and then pass to the south of the capital, which is home to some 13 million people and is hosting thousands of athletes for the regional Southeast Asian Games.
Airport officials said they made the call based on the potency of the storm, which was forecast to come ashore with intense rains and sustained winds of up to 165 kilometres (100 miles) per hour as well as gusts of up to 230 kilometres per hour, forecasters said.
Nearly 70,000 people had already fled their homes in the Bicol region, disaster officials said, which is where the typhoon is expected to strike first.
However, some residents opted to stay put even as the storm's power began to hit.
The weather bureau also warned of rain-induced landslides and possible storm surges of up to three metres (10 feet) which could hit coastal areas in the nation's east.
The Philippines is hit by an average of 20 storms and typhoons each year, killing hundreds and putting people in disaster-prone areas in a state of constant poverty.
The country's deadliest cyclone on record was Super Typhoon Haiyan, which left more than 7,300 people dead or missing in 2013.