By a number of yardsticks, relations in the Taiwan Strait today are the best they’ve been in years, if not ever. But if a report released by Taiwan’s Ministry of National Defense (MND) on Friday is any indication, Taiwanese government officials don’t appear to be convinced that such détente will last for very long.

Without doubt, the pace of normalization in relations between Taiwan and China, especially at the economic level, has accelerated dramatically since Ma Ying-jeou of the Chinese Nationalist Party (KMT) was elected in 2008, a process that is expected to continue with Ma securing a second four-year term in January. In addition to the landmark Economic Cooperation Framework Agreement (ECFA) signed in June 2010, the governments on both sides have inked at least 16 agreements touching on various aspects of cross-strait relations, including an agreement reached on Friday that will allow banks in Taiwan to clear renminbi transactions, a move that obviates the need for converting the currency into U.S. dollars before a transaction can be made.

Beyond trade, visits to Taiwan by Chinese officials have become almost routine, a limited number of Chinese can now study at Taiwan’s universities, Chinese tourism to the island has boomed, and joint exercises by the countries’ respective coast guards are now held every other year since 2010, mostly for the purpose of sea-rescue operations in the waters off Taiwan’s Kinmen and China’s Xiamen.

While those developments have for the most part contributed to a less tense, if not amicable, environment in what was once regarded as a potential tinderbox, Taiwanese officials are aware that Beijing remains committed to far more than economic liberalization. What it wants and has made no secret of is unification. Interestingly, during Ma’s first term as he was attempted to create a new paradigm in relations with China, government agencies, including the MND, found it very difficult to say anything publicly that was too critical of China. This, we can assume, was under directions from top officials in the Presidential Office, who feared that hostile rhetoric — such as pointing out that, despite better relations, China was continuing its missile build-up targeting Taiwan — would undermine his efforts at rapprochement.

For one reason or another, that restraint seems to have disappeared. Officials are now making it clear that military exercises, for example, are targeted at China and not at “nature” or some abstract enemy. Last week’s report to the Legislative Yuan on the five-year modernization plan for the armed forces’ military capabilities went one step further by claiming, reportedly for the first time in such a report, that China “may attempt a direct assault on Taiwan proper” once it has acquired enough amphibious transport vehicles or when the situation calls for it.

Additionally, the report said the People’s Liberation Army (PLA) had been hard at work improving its electronic warfare (EW) capabilities so that it can operate in a complex EW environment, while pointing to signs that China could turn to all-put psychological warfare to sow confusion in Taiwan ahead of a military campaign.

The report also states that the MND was expanding its Communication Electronics and Information Bureau (CEIB) to include a specialist group on electronic and cyber warfare. This was in direct reaction to sustained cyber-attacks against Taiwan’s government and national security systems originating from China. Emphasizing this point, Taiwan’s National Security Bureau (NSB) said that in the January-to-June period, its computers had been the targets of more than 1 million cyber-attacks, the great majority coming from China.

Such signaling, which was immediately picked up by the local media, could not have been made without the consent of senior government officials. Several factors can help explain why Taiwan is hardening its position. These include the need for increased military preparedness ahead of the expected pressure from Beijing for the two sides to enter sensitive political negotiations. Already there are signs that China has begun turning the screws on this issue.

Another possibility is that Taipei may have realized that despite the recent “goodwill,” China will not abandon the military option and will continue to widen the balance of power in its favor, which increases mistrust. Uncertainty about the regional environment amid rising tensions in the East and South China Sea, added to the U.S. “pivot” to Asia, could also explain that shift, perhaps even signaling Taiwan’s “choosing sides” as Beijing tries to give the impression that the two cooperate in defending territorial claims in those two areas (claims that Taipei has systematically denied).

Other possible factors include institutional turf battles and efforts by the MND to obtain a greater share of next year’s government budget, especially at a time when it embarks on a hugely expensive program to create an all-volunteer base force by 2015. Or this could be part of a strategy to send a signal of commitment to Washington ahead of the U.S. presidential election and to play Republicans against Democrats with a view to future arms deals. With the “China threat” a prominent feature of the campaigns there, Taiwan could see this as an opportunity to secure future military assistance deals with the U.S.

Whatever the reason, Taipei is fully aware that Taiwanese prefer the “status quo” to unification with China, especially one that continues to be governed by an undemocratic and repressive regime. Unless he intends to disregard the wishes of the 23 million people who put him in power — which includes the majority of people who voted for him, who also do not desire unification — Ma has little option but to prepare for a rainy day. Since Beijing has shown no intention to abandon the military option, even after four years of détente under a very accommodating, if not pliant, administration in Taipei, Taiwan’s response has to be in kind.

The signaling may be a subtle shift, but it’s a step in the right direction. This by no means signifies that Taipei should abandon efforts to improve relations with China — quite the contrary. But not knowing how an increasingly nationalistic and assertive Beijing will react when cross-strait relations enter a more difficult period, as they certainly will, or when Chinese claims butts heads with Taiwan’s own nationalism, Taiwan cannot afford to let its defenses down. A strong defense is the best insurance Taiwan can buy at this point.