Taiwanese protesters scuffled with police on Thursday ahead of China's launch of a controversial flight route, which they say has been allowed to go ahead despite fears over security risks.

The route over the Taiwan Strait is due to be inaugurated on Sunday, despite a backlash over security concerns.

Around 40 protesters entered the lobby of the headquarters of the Mainland Affairs Council (MAC) -- Taiwan's top China policy-making body -- in the capital Taipei to voice their anger.

The demonstration comes as fears grow over increasing influence from Beijing.

"The Chinese side unilaterally drew up the M503 route and the MAC failed to defend Taiwan's sovereignty to agree to it. We demand M503 be retracted as it posts security concerns for Taiwan," said protest spokesman Lin Yu-lun.

Protesters scuffled briefly with police before being forced outside where they gathered until a MAC representative accepted a protest letter.

There were no arrests, police said.

M503 is one of four routes which would take planes over the Taiwan Strait from China's coastal province of Zhejiang and the cities of Fuzhou and Xiamen in Fujian province.

Beijing says they are necessary to ease congestion on an existing flightpath.

But Taiwan's authorities have slammed the unilateral move and said it poses a potential air defence threat.

The route was originally due to be launched on March 5, but was postponed due to those objections.

China later slightly modified M503 but is pressing ahead with the launch.

The other three routes have been indefinitely postponed, according to Taiwan's Civil Aeronautics Administration.

The MAC has said the negotiations with China over the routes will help safeguard the island's aviation security.

It has also said that Chinese fighter jets would not use the routes.

China considers self-ruled Taiwan a part of its territory awaiting reunification -- by force if necessary. They split in 1949 at the end of a civil war.

Cross-strait ties have improved markedly since President Ma Ying-jeou of the China-friendly Kuomintang party came to power in 2008, but some fear Taiwan is becoming over-dependent on the mainland.

Thursday's protest comes a week after campaigners gathered to mark the anniversary of the student-led "Sunflower Movement", which occupied the island's parliament for more than three weeks last year over a trade pact with China.

Campaigners are now calling for a halt to the latest round of negotiations with China on another trade pact, scheduled for next week in Beijing.