"We shall let the lower echelon people to try to manage or solve the problems one by one," he said.
He did say, however, that "when the time comes we will consider whether we will have the kind of a sort of state visit but it is very difficult because of the relationship between Taiwan and the mainland is rather sensitive".
Ma, who campaigned on a platform of establishing closer economic links and signing a security pact with China, described Beijing as a threat but also an opportunity.
"If they [China] still squeeze Taiwan that will certainly give encouragement to the Taiwan independence movement"
Ma Ying-jeou, Taiwan's president elect
He urged Beijing not to "squeeze" Taiwan so that ties could improve.
"If they still squeeze Taiwan that will certainly give encouragement to the Taiwan independence movement, which they don't like very much," he said.
China has a long-standing policy of encouraging other nations to recognise Taiwan as being part of China.
Only 24 nations presently recognise Taiwan diplomatically, a quarter of these developing nations in the South Pacific.
Beijing has claimed Taiwan as its territory since nationalist Kuomintang (KMT) forces fled to the island from in 1949 following the communist victory in the civil war.
China's growing deployment of missiles along its coastline facing Taiwan - presently thought to number more than 1,000 – makes Taiwan's sovereignty a serious issue.
"As to the question of Taiwan's sovereignty, this is something that we may not be able to see the solution", said Ma, who was formerly KMT chairman and mayor of the Taiwanese capital of Taipei.
Ma reiterated his support for "normalising" Taiwan's ties with the mainland in economic, cultural and security terms.
|China has not ruled out using its military|
to reunify with Taiwan [GALLO/GETTY]
But he ruled out the chances of Taiwan joining the mainland in a similar autonomous arrangement as Hong Kong.
"It is very clear that we will never give up our system and to be reunited with them (the mainland) so this is something that we insist. We cannot solve the sovereignty issue but we can manage it" he said.
Ma, who won a landslide victory, is widely seen as being far closer to China than Chen Shui-bian, the outgoing president with the Democratic Progressive Party.
Ma said he would push for regular charter flights between across the Taiwan Straits, mainland tourists visiting Taiwan, two-way capital flows, and social and educational exchanges.
Before the election, Ma insisted that closer ties between Taiwan and China was the only way to boost Taiwan's economic performance.
Taiwan has lagged during recent years in comparison with a number of its "little dragon" peers such as Singapore and Hong Kong.
Although supporting closer China-Taiwan ties, Ma did not shy away from offending China's sensitivities over its human rights record and its Tibetan problem.
Taiwan 'not Tibet'
The president elect called on China to stop suppressing Tibetan people and to open talks with the Dalai Lama, who "hasn't advocated violence and hasn't advocated the complete independence of Tibet".
Ma said he took particular exception to recent Chinese statements referring to both Tibet and Taiwan as being China's "sacred territories".
"Taiwan is a democratic, prosperous country so it is very different from either Hong Kong or Tibet", he said.
While Ma has eschewed any top-level meetings with Chinese leaders in the near future, reports on Thursday indicated his in-coming vice-president could soon meet with Hu Jintao, China's president.
Vincent Siew flies to the Boao economic forum in the southern Chinese island of Hainan on Friday.
Siew has met China's president several times before in a private capacity.
It is possible to see the full interview with Ma Ying-jeou on 101 East broadcast, daily starting, on Thursday at 14:30GMT.