This is his first visit to the South after taking office.
In Narathiwat, he was updated about the flooding situation in the region before meeting with flood victims and presenting them with necessities.
In the afternoon, he flew to Phang Nga naval base to preside over the memorial service for victims..
The two-day memorial service, beginning today, will be held in Phang-nga’s Takua Pa district.
Thailand saw 5,395 people killed in the disaster - half of them foreign holidaymakers.
Gen Prayut told journalists briefly before his departure that he would follow up on the early warning system to prevent such tragedy from reoccurring in the future and would confer with Narathiwat governor on plans to establish special economic zones along the border with neighbouring countries.
Touching on the current flooding in several southern provinces, Gen Prayut said the severe changes in weather have resulted from the heavy use of natural resources. He also said he had ordered officials to store water after the floods recede for use in the dry season.
He said provincial governors and other concerned officials must be responsible if no water is stored once the floodwater receded.
Conveying his concern to neighbouring Malaysia which is experiencing massive floods, Gen Prayut said the government would dispatch necessities to that country because “both countries have good relations.”