On Friday the Indonesian navy's KRI Tedung Naga collided several times with Malaysia's KD Rencong near a reef off the coast of Borneo island where Indonesia is building a lighthouse.
"For the time being there will be no reinforcement. We will remain at our current position and our seven warships will also be maintained there," said Indonesian Navy Chief Vice Admiral Slamet Subiyanto, quoted by the Detikcom online news service.
Subiyanto also said the navy has no plans to seek the help of the army or air force, and the Indonesian government wants to avoid any open conflict with Malaysia in the Ambalat maritime area.
The navy spokesman could not be reached for comment.
But Kompas newspaper said the two ships brushed against each other at least three times on Friday, damaging the port side of the Indonesian ship and the bows of the Malaysian vessel.
The Eastern Fleet Taskforce Commander, First Admiral Suparno, told Kompas the Indonesian vessel had warned the Malaysian ship against approaching the lighthouse being built by Indonesia on Unarang reef.
Last month officials from Indonesia and Malaysia began negotiations to settle the dispute over the area. They are to meet again in May.
Warships from both countries have come into close contact several times since February 16 when Malaysia's state oil company Petronas granted Shell a concession in the area.
Indonesia says the blocks awarded by Petronas are not in Malaysia's territory.
The two countries have locked horns over the region before. A dispute over the ownership of two islands ended in December 2002 with an International Court of Justice ruling that the islands belong to Malaysia.
Indonesia waged a limited war against Malayan and British forces over the future of Borneo island in 1963 after the British relinquished control. The conflict known as Konfrontasi (Confrontation) ended three years later as Jakarta focused on internal problems.