Mr Najib's assurance came eight days after the Aug 31 incident in which suspected insurgents burned Thai flags and hoisted hundreds of Malaysian flags across Thailand's southern border provinces.
Aug 31 marked the anniversary of the 1989 founding of an umbrella separatist group and the anniversary of Malaysia's independence from British rule.
The Malaysian leader also supported a peaceful solution in the strife-torn region that also focused on improving people's quality of life, Prime Minister Yingluck Shinawatra said after a meeting yesterday with Mr Najib on the sidelines of the Asia-Pacific Economic Cooperation (Apec) meeting in Vladivostok.
Ms Yingluck also had talks with Russian President Vladimir Putin and Chilean President Sebastian Pinera.
The relationship between Thailand and Malaysia remains strong despite the events of Aug 31, which were seen as an attempt to weaken relations between the two nations, the Thai premier said.
"Thailand has reiterated that it will continue to take care of the people in the deep South, including Malaysian nationals. Malaysia is also aware of the progress and supports the development," Ms Yingluck said.
She said Mr Najib supported Thailand's plan to set up more border checkpoints and strengthen security operations along the border ensure the safety of citizens from both countries and tourists.
Ms Yingluck also said that both countries had agreed to find long-term solutions to problems involving people with dual nationality.
The issue will be among the topics discussed during the Joint Commission in Malaysia next month, she said.
After the meeting with Ms Yingluck, Mr Najib said Thailand is taking steps to stabilise its southern region, the Bernama News Agency reported.
The steps were focused on education, training and the provision of assistance to small traders in the region.
Mr Najib said Malaysia would also cooperate with Thailand on the issue of falling rubber prices.
"We need to work together with Indonesia, under the International Tripartite Rubber Council," he said. Mr Najib added that a joint commission foreign ministers meeting would be held next month on the rubber issue.
Meanwhile, in Bangkok, Democrat Party leader Abhisit Vejjajiva yesterday warned that Deputy Prime Minister Chalerm Yubamrung's proposal for the election of provincial governors in the three southernmost provinces would create confusion among the locals.
"The idea could also create discontent among the people in the deep South and trigger a new conflict if the government fails to materialise the idea," Mr Abhisit said.
Mr Chalerm proposed on Friday that the governors of Yala, Pattani and Narathiwat provinces be elected so as to better deal with the southern unrest. The provinces would also have some degree of autonomy similar to the situation with the Bangkok Metropolitan Administration and Pattaya City.
"The southern issue is a highly sensitive one, so the government must be careful when proposing anything to the public, or it could create confusion just like when the idea of Nakhon Pattani was proposed," Mr Abhisit said, referring to the establishment of a special administrative zone proposed by former premier Chavalit Yongchaiyudh years ago.
Ahmadsomboon Bualuang, an academic in Pattani, supported Mr Chalerm's idea of elected governors, but urged the government to gauge opinion from local people before pressing ahead with the initiative.
He echoed Mr Abhisit's warning that the proposal of any policies on the deep South for political gain would only worsen the problem.
"Gen Chavalit floated an idea about Nakhon Pattani, while Prime Minister Yingluck said during her election campaign that she would turn the deep South into a special administrative zone if Pheu Thai becomes the government. But nothing has happened," the academic said.