The Malaysian premier made the statement after greeting the Thai premier on her one-day official visit. They held bilateral talks on various issues.
Speaking at a joint news conference with his Thai counterpart, Mr Najib said he hoped the Thai government would provide more economic development and opportunities for southern people.
"We both agree that this is a domestic matter for Thailand and that the people in the south must not seek a separate state," the Malaysian leader was quoted by the Malaysian newspaper The Star as saying at his office here.
Mr Najib also reiterated that Malaysia opposed violence in all forms—whether insurgent attacks or state suppression.
Most people in Thailand's Muslim-predominant southern border provinces of Yala, Pattani and Narathiwat share a common language, religion and culture with ethnic Malay Muslims across the border. Thai officials in the past accused Malaysia of giving the insurgents training and other aid. Malaysia denied such charges. The eight-year insurgency has seen more than 5,000 people died since early 2004.
Ms Yingluck’s visit is part of an introductory visit to a fellow member of the 10-nation Association of Southeast Asian Nations (ASEAN). It was earlier scheduled for last October but postponed due to nationwide flooding in Thailand.
The Thai premier said both leaders pledged to boost cooperation between the two countries including arrangements for the 12th Thai-Malaysian Joint Committee meeting.
Mr Yingluck stated the cooperation also included the development of economy, basic infrastructure, as well as the well-beings of Thailand's south and Malaysia's northern and eastern regions under the framework of the Thailand-Malaysia Committee on Joint Development Strategy for Border Areas (JDS).
Two bridges crossing the Sungai Kolok River will be constructed at Narathiwat's Sungai Kolok and Tak Bai districts, as part of the strategy to build stability and prosperity along the Thai-Malaysian border, according to the Thai prime minister.
"Thailand and Malaysia agreed to cooperate in the Halal food industry as Thailand has strength in agricultural and food processing industries, while Malaysia won international acceptance for its Halal food quality which meets international standards," said the Thai premier.
"There will be matching partners between operators of Small- and Medium-Enterprises in southern Thailand and northern Malaysia."