Thirty-odd members from the radical anti-China opposition party Taiwan Solidarity Union (TSU) attempted to push their way through a police line that guarded the entrance of a shrine where President Ma Ying-jeou was visiting.
After chanting slogans like "Ma Ying-jeou betraying, humiliating country" and a series of tussles with police, several of the demonstrators broke through the line but were blocked from going further.
"People of Taiwan by no means accept M503," a protest leader said, referring to the new route near the middle of the Taiwan Strait which separates the island from mainland China.
Holding protest signs, the crowd angrily pelted eggs and slippers at Ma's motorcade, but the projectiles fell short.
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No one was injured or arrested in the clash.
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, prompting China to postpone the inauguration of M503 and move it slightly closer to the mainland.
The run-up to today's route launch saw protesters scuffle with police, and the arrest of 13 demonstrators who splashed red paint on the walls of the presidential residence.
The government has said that 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 M503.
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.
Ties have improved markedly since Ma came to power in 2008 on a China-friendly platform, but some fear Taiwan is becoming over-dependent on the mainland.