Together with Pedra Branca and another rock formation within the vicinity known as South Ledge, Middle Rocks were the subject of a territorial dispute between Malaysia and Singapore. For Middle Rocks and South Ledge, the dispute arose when Singapore claimed both islets in 1993. The matter was settled by the International Court of Justice in 2007, which ruled that Middle Rocks belonged to Malaysia and Pedra Branca to Singapore. The status of South Ledge remains unresolved. Following the decision, Singapore and Malaysia said they would hold discussions to establish the maritime border around the area. Both countries established the Malaysia-Singapore Joint Technical Committee to implement the court's judgement. According to Malaysia, the MSJTC reached an impasse in November 2013. Malaysia clarified that one of the key reasons is that "the parties have been unable to agree over the meaning of the 2008 judgement as it concerns South Ledge and the waters surrounding Pedra Branca. Malaysia sent a team from its Mapping and Survey Department which constructed a flag pole, five markers and a monument between 4 and 12 June 2008. The Malaysian flag was raised and the team sang the Malaysian national anthem, Negaraku, during a ceremony which was covered by the press on 13 and 14 June 2008.
On 5 August 2017, Jane's Defence Weekly reported that Malaysia had established a new maritime installation, the Abu Bakar Maritime Base, on Middle Rocks, which consists of two clusters of rocks located 1 kilometre south of Pedra Branca that Malaysia is currently challenging. The base, built across the eastern opening of the Strait of Singapore, comprises a 316-metre jetty, a helipad, and a lighthouse. According to the Sultan of Johor, the installation, which is a project under the auspices of the National Security Council, "is aimed at safeguarding Malaysia's sovereign territory and waters, and for conducting marine scientific research". The base also seeks to reaffirm "Malaysia's absolute sovereignty over the Middle Rocks". On 11 August, Malaysia deployed a missile-capable fast-attack craft Perdana to its new Maritime Base on the Middle Rocks. Royal Malaysian Navy chief Admiral Ahmad Kamarulzaman Ahmad Badaruddin confirmed the deployment when he posted photographs of Perdana's arrival at the base. Photos posted by the Navy chief showed two armed guards on an observation deck, as well as a communications system fitted with surveillance equipment, as pointed out by Jane's Defence Weekly. In late May 2018, Malaysia announcing their plan to convert Middle Rocks into an island. In announcing Malaysia's plans on the week of 2 Jun 2018, Dr Mahathir said: "We have already built features there on Middle Rocks. Our intention is to enlarge it so that we can form a small island for us. He added "That is something we are thinking of." When pressed to clarify Malaysia's plans, he said: "We haven't made a full decision yet." When asked about Malaysia's plans to expand Middle Rocks, a spokesman for Singapore's Ministry of Foreign Affairs said: “Sovereignty over Middle Rocks belongs to Malaysia. We have no comments on Malaysia’s activities on Middle Rocks as long as they are in accordance with international law.”
