The protesters from the small anti-China opposition party Taiwan Solidarity Union briefly scuffled with military police guarding the residence of President Ma Ying-jeou in Taipei in the early morning.
The demonstration came ahead of the scheduled launch of the route known as M503 over the Taiwan Strait tomorrow.
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.
But Taiwan's authorities have slammed the unilateral move and said it poses a potential air defence threat.
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Earlier this week, protesters clashed with police as they tried to enter government buildings in two demonstrations in a row ahead of the scheduled launch.
The protesters arrested Saturday were later released after questioning.
Each was fined Tw$6,000 ($193) for violating a waste disposal law. Eight protesters also faced charges of interfering with public functions over the clash, a police officer said.
"Ma Ying-jeou sells out Taiwan," one protester shouted in footage aired by local television.
The route was originally due to be launched on March 5, but was postponed due to those objections.
China later slightly modified the M503 route but is pressing ahead with the launch.
The other three routes have been indefinitely postponed, according to Taiwan's Civil Aeronautics Administration.
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.
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.