By Neil Jerome Morales and Adrian Portugal

MANILA (Reuters) - Heavy rain from Typhoon Gaemi has flooded the Philippine capital Manila and nearby cities, forcing authorities to shut schools, offices and cancel flights on Wednesday and declare a state of calamity in a region that is home to 13 million people.

The storm, which is strengthening as it gusts towards Taiwan, did not make landfall in the Philippines but has intensified seasonal monsoon rains, causing landslides and flooding over the past few days.

At least 12 people have died and more than 600,000 are displaced due to the storm, known locally as Typhoon Carina, the national disaster agency said. Water in some areas is neck-high.

The Philippine coastguard said 260 passengers and 16 vessels were stranded in ports while airlines cancelled 114 flights out of Manila on Wednesday, the airport authority said.

The financial markets were also closed.

President Ferdinand Marcos Jr told the disaster relief agencies to provide assistance and prepare supplies for isolated communities during a briefing on Wednesday, and the mayors of 16 cities in the Greater Manila region have asked for emergency funding, officials said.  

In the riverside city of Marikina, emergency workers waded through waist-deep waters and used rubber dinghies to rescue residents from their inundated homes.

Some people sheltered in churches among the statues of Catholic saints.

"The flood reached the second floor of our house, all our things are ruined, everything got wet, nothing was saved," Ladylyn Bernas, an evacuee at a nearby church, told Reuters.

Social media posts showed several vehicles stuck in water or floating down streets and highways.

The Philippines sees an average of 20 tropical storms annually, causing floods and deadly landslides.

(Reporting by Neil Jerome Morales and Karen Lema; Editing by Christian Schmollinger and Christopher Cushing and Miral Fahmy)