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.
Although Indonesia was not a party to these territorial disputes, Jakarta soon began to pay attention to the Natuna islands. This was especially so after China was reported to have included the oil-rich area into a map detailing its claims in the South China Sea.
The Indonesian government learnt of this in 1993, but took up the matter with China only in July 1995, when Foreign Minister Ali Alatas visited the country.
Mr Alatas said he believed that "the Chinese map is only an illustrative one and could not be seen as an attempt to establish an actual position".
But if the response of the Indonesian foreign minister was mild, that of the Indonesian military was not. Defence and Security Minister Edi Sudrajat was quoted as saying that the map featured parts of Indonesia's territorial waters around the Natuna islands and "was made without respect to international sea laws".
The Natuna islands issue was not completely resolved in the 1990s. But it was clear that both Beijing and Jakarta were treating the matter with caution.
In more recent years, however, Beijing's attitude towards the South China Sea issue has been hardening, as countries with claims in the area have issued permits to companies to begin exploring its resources.
Disputes over fishing rights were followed in 2012 by another conflict between Beijing and Manila over Scarborough Shoal.
In November 2012, Indonesia also expressed concern when China issued new passports which included a map of the South China Sea.
Last year, the Philippines referred its territorial dispute with China to the international tribunal, submitting the formal documents this month. China objected to the dispute being referred to the international court, preferring to resolve it bilaterally.
It was against this background that the Natuna waters issue was raised in Indonesia. Commodore Fahru expressed the objections of the Indonesian military to the Chinese map, and it was reported that the military had also decided to increase its defence capability on the islands.
Indonesia's foreign minister, however, has remained cautious in his statements. Indeed, the nation's defence and foreign ministries often take different attitudes.
As long as Indonesian territorial integrity is not affected, the foreign ministry will probably have the upper hand. The situation would be very different if China were to send its patrol vessels to the Natuna waters. But this is unlikely in the foreseeable future, given the current stage of Beijing- Jakarta relations.
The foreign ministry appears to believe that diplomacy is the best way to moderate China's assertiveness in the present circumstances.
It remains to be seen whether the strategy will achieve its objective.
The author is visiting senior fellow at the Institute of Southeast Asian Studies.
This article was published on April 24 in The Straits Times.Get a copy of The Straits Times or go to straitstimes.com for more stories.