The scuffle started when the speaker, Wang Jin-pyng, rejected an opposition bid by the pro-independence Democratic Progressive Party to have a detailed debate on the Economic Cooperation Framework Agreement, a contentious trade pact with China.
One side wanted to debate each clause of the agreement separately rather than consider the pact as a whole.
Wang's decision is almost certain to speed up the agreement's passage, which is already guaranteed by the Nationalists' heavy legislative majority.
The deal, which was signed last week in the Chinese city of Chongqing, is the jewel in the crown of President Ma Ying-jeou's two-year effort to tighten the bonds between Taiwan's high-tech economy and China's lucrative markets.
It is expected to go into effect in early 2011.
The Associated Press contributed to this story.