TAIPEI—Taiwanese police evicted dozens of protesters from the cabinet building early Monday morning, as tensions continued spiraling between the government and students occupying two major government buildings over a controversial trade pact with China.
Shortly after midnight, police made several attempts to remove protesters who stormed the Executive Yuan—the governing cabinet's office—on Sunday evening, hours after President Ma Ying-jeou rejected protesters' demand to retract a services trade agreement signed with China in Shanghai last year.
Antiriot police, wearing helmets and clutching shields, rammed through a human wall of protesters linked arm-in-arm to block the entrance of the Executive Yuan. In the midst of the brawl, some protesters held their hands up to show they meant no harm and were yanked away by police.
Police arrested 58 people for trespassing, and a dozen were injured in the scuffle, government-run Central News Agency reported. Police officials weren't immediately available for comment.
The Executive Yuan is a block away from the legislative building, which has been seized by thousands of students and protesters since Tuesday. Police haven't made any attempt to remove protesters there.
During a news conference in Taipei early Sunday, Mr. Ma—also the head of the ruling Chinese Nationalist Party, or the Kuomintang—said retracting the trade agreement would undermine Taiwan's credibility as a trade partner, and he dismissed concerns the deal would hurt small businesses.
"The pact must be passed for the sake of Taiwan's economic future," Mr. Ma said. He noted that Taiwan now has only seven free-trade partners, while its main export competitor, South Korea, already enjoys tariff-free treatment in more than 40 countries. "Signing free-trade agreements is an inevitable trend on which Taiwan can't afford to miss out," he said.
In a statement issued late Sunday, Mr. Ma condemned the violence and asked police to exercise all legal means to expel the protesters. He had said in his previous statements the government wouldn't evict protesters by force.
One of the student leaders, Lin Fei-fan, urged Mr. Ma to halt all eviction orders and asked protesters to fight by peaceful means.
"Don't let our hard work in the past week go down the drain," Mr. Lin told protesters. He added that the crowd that stormed the Executive Yuan did so on their own accord, and that their actions don't represent the student-led movement.
Earlier Sunday, one of the leaders, vowed to continue occupying the legislature's assembly hall until the students' demands are met. "The president has completely missed the point. Our demand is to retract the pact and establish a mechanism to monitor all cross-Strait deals in the future," said Chen Wei-ting.
Student protesters shout slogans in as they surround the legislature in Taipei, Taiwan, on Saturday.Associated Press
The protests have been among the island's most divisive since Mr. Ma came to power six years ago, promising to build closer economic ties between China and Taiwan, former antagonists in the decades-old Chinese civil war. According to Mr. Ma's government, the pact, which focuses on services, is an essential step to further liberalize cross-Strait trade and will provide select businesses with wider access to China's market.
Protesters, though, have demanded that the agreement be nullified and seized the meeting chamber of the Legislative Yuan on Tuesday. They argue that the deal will hurt small businesses and job prospects for people in Taiwan, especially the young. They say that the negotiations lacked transparency and that the deal may enable China to exert more influence over Taiwan's economy and politics.
Some opponents also fear that growing Chinese clout in self-ruled Taiwan may undermine the island's democratic system. Despite warming ties, Beijing hasn't retracted its vow to take back Taiwan, by force if necessary.
Dubbed the "Sunflower Movement," the students' seizure of the legislative chamber followed the KMT's unilateral passage of the pact during a first reading without bipartisan deliberation on March 17. Protesters interpret the KMT's move as backing away from its earlier commitment to the opposition Democratic Progressive Party to review the pact one clause at a time.
Three days into the occupation, the KMT softened its stance by agreeing to review the agreement line by line during the second legislative reading of the deal.
The protest, once numbering more than 10,000 people, is the biggest student-led protest in Taiwan's history. It is also the first time that the legislature has been taken over by protesters. Many professors have publicly stated their support for the students, agreeing to cancel classes for the duration of the protest.
Thousands of antiriot police are on the scene, but so far there have been no major altercations. The government said it won't forcefully evict the protesters but hopes the students end the occupation to allow the legislature to resume operation immediately.

(Note: This Wall Street Journal Article supports the pact and parts not related to the student protest have been deleted)
—Aries Poon contributed to this article