On March 12, Indonesia's Commodore Fahru Zaini, assistant deputy to the chief security minister for defence strategic doctrine, was reported to have said that "China has claimed Natuna waters as their (sic) territorial waters. This arbitrary claim... will have a large impact on the security of Natuna waters".
On March 18, however, Indonesian Foreign Minister Marty Natalegawa contradicted him.
"There is no territorial dispute between Indonesia and China," the minister insisted.
He pointed, instead, to ongoing maritime cooperation between China and Indonesia at the deputy foreign minister level. One of the projects, he said, involved direct foreign investment in Natuna for fish processing and canning.
But Mr Natalegawa did concede that Jakarta had rejected China's controversial "nine-dash line" in the South China Sea. It had also questioned China on the legal basis of the line without receiving any reply. But the minister insisted that all this had nothing to do with Natuna islands.
However, many observers, especially in the West, believe that Indonesia's position has changed.
Instead of being neutral, Indonesia has effectively sided with other South-east Asian claimants.
But is this really true? In order to get a fuller picture, let us look at the historical development of Indonesia-China relations, with special reference to the Natuna islands.
During the Sukarno years (1959-65), with the exception of the 1959 hiccup, relations were generally cordial. Towards the end of the Sukarno era, Jakarta and Beijing moved even closer to form an "anti-imperialism" partnership.
However, when General Suharto came to power (1966-98), the relationship soured. On Oct 31, 1967, Indonesia severed diplomatic ties with China. The two countries did not normalise ties until 1990.
After the fall of Suharto in 1998, bilateral relations improved further. Presidents Abdurrahman Wahid (Gus Dur), Megawati Sukarnoputri and Susilo Bambang Yudhoyono all visited China.
During the Yudhoyono presidency, Jakarta and Beijing even established special strategic partnerships.
An agreement was signed in 2005 and further enhanced to become a comprehensive strategic partnership when President Xi Jinping visited Indonesia last year. Jakarta was his first stop on a South-east Asian tour after becoming president of China.
Jakarta was unaffected by the territorial disputes in the South China Sea in the 1990s. Nevertheless, Indonesia, which perceived itself as the leader of the region, was concerned about the potential of the South China Sea issue to affect regional political stability.
Beginning in the late 1980s up to the mid-1990s, Indonesia initiated four informal workshops. At first, China refused to participate. But it sent delegates to these workshops after diplomatic ties were normalised.
During the ASEAN Foreign Ministers meeting held in July 1992 in Manila, China's Foreign Minister Qian Qichen suggested that a "China-ASEAN Forum" be set up to discuss the issue.
But ASEAN representatives were not interested, believing that there were enough forums available to deal with the issue. In March 1995, conflict over Mischief Reef in the South China Sea between Beijing and Manila led to renewed concern over Beijing's intentions.