Questions have been raised over Putrajaya's denial that its recent maritime agreements with Indonesia included the Ambalat block, a 15,000 sq km area at the heart of a territorial dispute off the coast of Sabah which is said to contain one of the biggest crude oil deposits in the world.
This comes after Deputy Foreign Minister Mohamad Alamin rejected a claim by Warisan assemblyman Assaffal Alian that Malaysia had surrendered its claim to Indonesia.
Instead, Alamin said the recent maritime agreements signed by Prime Minister Anwar Ibrahim and President Joko Widodo, hailed by both leaders as ending an 18-year dispute, had nothing to do with the Ambalat block or any other area more than 200 nautical miles from the Exclusive Economic Zone.
"We also have not negotiated on anything relating to the Ambalat border," he said yesterday.
An exclusive report by CNBC last month however said Malaysia and Indonesia would cooperate in exploiting the oil and gas resources in the Ambalat block.
The report on July 13 quoted Indonesia's director-general of oil and gas, Tutuka Ariadji, who said Indonesia and Malaysia would carry out a "desk study" on the oil exploration in Ambalat, an exercise to analyse data from both parties.
Tutuka said the maritime border agreement signed in June was an "indication of a closer cooperation to come", adding that the desk study, which will be completed by the end of this year, was better than the usual method of seismic surveys which he said could spark potential conflicts due to cross-border intrusions.
"Our position is advantageous because of the many islands," Tutuka told CNBC.
On June 8, Anwar and Jokowi signed a number of treaties including on the delimitation of territorial seas in the Sulawesi Sea and the Straits of Melaka, amid reservations from maritime experts over proposals to settle the dispute.
A day earlier, MalaysiaNow reported that maritime experts involved in efforts to protect Malaysia's territorial rights had warned Putrajaya against signing any new agreements to settle the long-running border dispute with neighbouring Indonesia.
They said Malaysia could not afford to compromise on its claims over disputed areas with Jakarta in the Sulawesi Sea and in the southernmost part of the Straits of Melaka.
When quizzed on the matter, Anwar said the agreements were not yet complete.
"Negotiations to complete the territorial boundary lines in the Sulawesi Sea are still ongoing. I told President Jokowi, Malaysia still insists it is Malaysia's, while Jokowi said that his experts told him they belong to him (Indonesia). So we have postponed and will continue discussions," the prime minister said in a reply in the Dewan Rakyat.
Jokowi, on the other hand, said the agreements had settled long-standing disputes with Malaysia.
"After 18 years of negotiations... praise be to God, it has finally been resolved," he was quoted as saying by AP during a joint press conference with Anwar.
The tussle over Ambalat, which Malaysia refers to as Block ND6 and Block ND7, has seen minor clashes between Malaysia and Indonesia, with the issue often included during anti-Malaysian protests in Indonesia.
In 2004, national oil firm Petronas' concession to Shell to explore oil and gas within the Ambalat area drew protest from Indonesia, which had also given a concession to Italian company ENI.
In 2008, Jakarta protested Malaysia's military presence in the area, and the following year, Indonesian navy ships reportedly came close to opening fire on a Malaysian navy patrol ship for ignoring orders to leave.
Indonesia has claimed ownership of the area by citing the Indonesia-Malaysia Continental Boundary Treaty signed in 1969 in Kuala Lumpur, despite the Ambalat block's location which borders directly with Malaysia. Malaysia later issued an official map which placed the Ambalat block in its territory.