Taiwan on Friday protested after China started issuing new passports with maps that feature two of the island's most famous scenic spots as part of Chinese territory.

Taiwan's President Ma Ying-jeou urged China not to "unilaterally damage the status quo of the hard-fought stability across the Taiwan Strait", his office said in a statement.

China's new computer-chipped passports are equipped with a map that covers Sun Moon Lake and Cingshui Cliff, both popular tourist destinations on Taiwan.

The Mainland Affairs Council, the island's top China policy-making body, stressed that Taiwan "is an independent sovereign country".

"China should recognise the facts that the two sides have ruled separately... and exercise self-restraint when faced with controversies," the council said.

China still regards Taiwan as part of its territory awaiting reunification, by force if necessary, even though the island has ruled itself since the end of a civil war in 1949.

Tensions lingered between the two sides for decades until Ma assumed the presidency in 2008 on a Beijing-friendly platform, adopting a series of policies to boost trade and civil exchanges.

China's new passports also provoked protests by the Philippines and Vietnam for showing various islands in the South China Sea as being in its territory despite overlapping sovereignty claims.

Beijing attempted Thursday to downplay the diplomatic fallout from the recently introduced passports, with a foreign ministry spokeswoman saying the maps were "not made to target any specific country".