He expressed condolence to families of the two soldiers who died after Thai and Cambodian troops exchanged fire on the disputed border area on Friday.
He said the border dispute had prolonged, since both sides had different views on the line of demarcation.
The prime minister said he respected the ruling of the International Court, after it awarded the ruins to Cambodia in 1962.
However, he admitted that the situation had intensified after Cambodia applied to list Preah Vihear as a World Heritage site and asked Thailand for approval.
Troops from both sides then gathered near the ancient temple. Until recently, a Thai soldier stepped on a landmine, and the two countries claimed that the land belonged to them.
Mr Abhisit said the government had discussed this with Cambodian high-ranking officials, and he and Cambodia's Prime Minister Hun Sen both agreed that the Joint Border Committee to continue negotiations.
He said Deputy Prime Minister overseeing security affairs Suthep Thaugsuban and Defence Minister Pravit Wongsuwan were continually coordinating with Cambodian authorities.
The Thai government will do its best to protect the country's territorial sovereignty, and this issue will be raised at the Association of Southeast Asian Nations (Asean) Plus Three and Plus Six summit, scheduled to be held in Pattaya this month.