In some areas, water reached the rooftops of buildings, where some residents had sought refuge.
"It is the most devastating flooding in more than 30 years in Phu Yen," the national disaster committee said in a statement, after part of the province's system of dykes was overwhelmed.
Local television reported on Wednesday that thousands of people were stranded in pagodas, schools and other public buildings in Phu Yen, unable to reach their homes.
Pascal Bourcher, operations manager for the International Federation of the Red Cross and Red Crescent in Hanoi, told Al Jazeera that more than 260,000 people had been evacuated.
Supplies running short
Morakot - early August
Over 130 people killed as it lashed Taiwan. Mudslides destroyed thousands of homes in the south.
Ketsana - late September
Deadly floods in the Philippines killed at least 337 people. Thousands also displaced and homes destroyed in and around the capital Manila. Ketsana also lashed Vietnam, leaving at least 170 dead
Parma - early October
Fresh floods hit most of the northern Philippines left atleast 540 people dead.
Lupit - late October
Approached near northern tip of the Philippines, caused heavy rains.
Mirinae - early November
Fourth typhoon to hit the Philippines, bought heavy rain to already saturated capital.
Local authorities in the Phu Yen province have requested emergency food and drinking water from the central government in Hanoi after supplied started to run low.
According to a UN report citing Vietnamese authorities, Mirinae destroyed 900 homes and damaged more than 14,000 others while some 18,000 hectares of rice land was flooded.
Before making landfall in Vietnam on Monday, Mirinae had had previously hit the Philippines as a typhoon, leaving at least 27 people dead.
Over 16,000 people are still living in evacuation centres.
Mirinae also killed two people in neighbouring Cambodia.
Vietnam and the Philippines are frequently hit by tropical storms and flooding this time of the year and both countries were hit hard by Typhoon Ketsana in September.
Ketsana caused one of Vietnam's worst disasters in recent years, leaving more than 170 dead and hundreds injured.
It also caused devastating floods, inundated hundreds of thousands of homes and damaged tens of thousands of hectares of rice and other crops.