President Mamun Abd al-Qayum's office said rescue teams had evacuated 10,000 people from the worst hit of the low-lying cluster of the Indian Ocean atoll islands.
The chain of 1200 tiny palm-fringed coral islands dotted 800km off the toe of India stand just a few feet above sea level.
Abd al-Qayum has spent much of his 26 years in power warning of the dangers that global warming, erosion and shifting weather patterns pose to low-lying island nations like his own.
And with two-thirds of the capital under water, chief government spokesman Ahmad Shahid said there was no choice but to declare a state of emergency and delay controversial elections.
The elections commission said on Tuesday the vote would be rescheduled for 22 January. The vote is seen as a crucial test for the 67-year-old head of state - the longest serving leader in Asia who has headed the nation of 330,000 Sunni Muslims since 1978.
The Maldives government does not recognise any political party and candidates must offer themselves for elections as independents.
The election is for 42 seats in the 50-member national parliament where eight members are nominated by the president.
Although political parties are not allowed to campaign, dissidents have put forward proxy candidates to challenge Abd al-Qayum loyalists at the vote.
The president cracked down on dissidents in August after imposing a state of emergency which lasted for two months. Key dissidents remain in jail or under house arrest.