Taiwan has banned its senior officials from studying in China for "national security" reasons in the latest dispute overshadowing improved ties with China, an official said Wednesday.

The interior ministry's administrative order is effective from Thursday.

"The new measures have been adopted due to national security considerations," an official from the National Immigration Agency told AFP.

"We're worried that confidential information available to high-level government officials might be leaked as they write their theses and research papers," he said on condition of anonymity.

Local media said dozens of people may be forced to suspend academic programmes on the mainland.

Relations between China and Taiwan have improved markedly since President Ma Ying-jeou came to power in Taipei in 2008, but have recently hit turbulence.

The Global Times, a newspaper controlled by the Chinese communist party, recently accused Taiwanese intelligence authorities of trying to recruit Chinese students studying on the island to spy on the mainland.

It said Chinese authorities had uncovered more than 40 such cases in 15 provinces, charges denied by the Taiwanese authorities.

Fan Liqing, spokeswoman for China's Taiwan Affairs Office, said the moves by Taiwan intelligence authorities "have seriously harmed the safety and health of young students and gravely disturbed the educational cooperative exchanges between the two sides".

The Taipei-based United Daily News suggested Wednesday the spying charges could be a reprisal for Taiwan's investigation in August into a former top official handling China policy, who is now accused of leaking state secrets.

Chang Hsien-yao, an ex-deputy minister at Taiwan's Mainland Affairs Council, stepped down in August over allegations he leaked confidential work-related information. The case is still under investigation, while he has denied the charges.

The News said Beijing was also unhappy after Ma twice publicly threw his weight behind Hong Kong's pro-democracy protesters.

Taiwan and China split in 1949 at the end of a civil war but Beijing still sees the island as a renegade province awaiting eventual reunification.