It said an active monsoon trough is covering the lower North and Northeast until Friday, while the southwest monsoon trough continues prevailing over the Andaman Sea, Thailand and the Gulf of Thailand.
The department expects more rain across the country, with isolated heavy to very heavy rain in the North, Northeast, East, South and Central region, including Greater Bangkok.
Strong winds are expected to create 2-3 metre high waves in the upper Andaman Sea and the upper Gulf of Thailand and even higher during thundershowers.
Waves in the lower Andaman are expected to rise about 2 metres high, and higher during thundershowers.
The department warned people to beware of flash floods and overflows. Ships have been advised to proceed with caution and avoid thundershowers while small boats in the upper Andaman Sea and the Gulf are advised to stay onshore until Friday.
The affected areas are as followings:
Tuesday to Wednesday
North: Mae Hong Son, Chiang Mai, Lamphun, Lampang, Phrae, Sukhothai, Uttaradit, Tak, Kamphaeng Phet, Phichit, Phitsanulok and Phetchabun.
Northeast: Loei, Nong Bua Lamphu, Udon Thani, Chaiyaphum, Khon Kaen, Kalasin, Mukdahan, Maha Sarakham, Roi Et, Yasothon, Amnat Charoen, Nakhon Ratchasima, Buri Ram, Surin, Si Sa Ket and Ubon Ratchathani
Central: Nakhon Sawan, Uthai Thani, Chai Nat, Singburi, Ang Thong, Ayutthaya, Lopburi, Saraburi, Kanchanaburi, Suphan Buri, Ratchaburi, Nakhon Pathom, Samut Songkhram and Samut Sakhon including Greater Bangkok
East: Nakhon Nayok, Prachinburi, Sa Kaew, Chachoengsao, Chonburi, Rayong, Chanthaburi and Trat.
South: Phetchaburi, Prachuap Khiri Khan, Chumphon, Surat Thani, Ranong, Phang Nga, Phuket and Krabi.
Thursday to Friday
North: Mae Hong Son, Chiang Mai, Chiang Rai, Lamphun, Lampang, Phayao, Phrae, Nan, Sukhothai, Uttaradit, Tak, Kamphaeng Phet, Phichit, Phitsanulok and Phetchabun.
Northeast: Loei, Nong Bua Lamphu, Nong Khai, Bueng Kan, Udon Thani, Sakon Nakhon, Nakhon Phanom, Chaiyaphum, Khon Kaen, Kalasin, Maha Sarakham, Roi Et, Nakhon Ratchasima, Buri Ram, Surin, Sisaket and Ubon Ratchathani.
Central: Nakhon Sawan, Uthai Thani, Chai Nat, Sing Buri, Ang Thong, Ayutthaya, Lopburi, Saraburi, Kanchanaburi, Suphan Buri, Ratchaburi, Nakhon Pathom, Samut Songkhram and Samut Sakhon including Greater Bangkok
East: Nakhon Nayok, Prachinburi, Sa Kaew, Chachoengsao, Chonburi, Rayong, Chanthaburi and Trat.
South: Phetchaburi, Prachuap Khiri Khan, Chumphon, Ranong, Phang Nga and Phuket
From Saturday to Sunday, the monsoon trough will move across the North and the Northeast while the moderate southwest monsoon will cover the Andaman Sea and the Gulf of Thailand, causing heavy rains in some areas in Thailand.
The department added that the Hinnamnor typhoon is heading to South Korea and Japan, and will not affect Thailand.