Around 200 student-led demonstrators have occupied parliament for more than a week and are urging people to take to the streets of Taipei Sunday to increase the pressure on Ma's Kuomintang government.
In a bid to placate demonstrators Ma, who has sought closer ties with China since becoming the island's leader in 2008, said he would agree to demands that a law be introduced to monitor all agreements with China.
"I want to make a clear promise here, I support the legalisation of the mechanism," he said in a speech broadcast live on television as thousands of supporters took to the streets demanding the protesters leave parliament.
"I also want to urge the ruling and opposition parties to complete the task before the end of this legislative session."
However Ma, rejected the protesters main demand -- that the service trade agreement signed with China in July last year be retracted.
"We support the agreement to be debated and voted clause by clause, but I oppose the idea of retracting the agreement.
"It would cause too much damage to Taiwan. It would cost Taiwan's international credibility.
"In the future, no one would trust Taiwan while holding similar negotiations."
Student leader Lin Fei-fan described Ma's offer as "no substantial guarantee" and renewed a call for a peaceful rally Sunday, which organisers hope will attract up to 100,000.
The pact is designed to open up further trade in services between China and Taiwan, which split 65 years ago after a civil war.
But the protesters say the deal will damage Taiwan's economy and leave it vulnerable to political pressure from China.
The protestors occupied parliament on March 18 and swiftly drew a large crowd of supporters, with more than 10,000 congregated outside the building at one point.
A group of radicals on March 23 stormed the nearby government headquarters but were dislodged by baton-wielding police and water cannon.
The violent dispersal of the protesters has added to the tensions.
Ma, whose approval ratings sit around 10 percent, has warned that failure to ratify the pact would be a grave setback to trade-reliant Taiwan's efforts to seek more free trade agreements and avoid isolation as regional economic blocs emerge.
The deal is a follow-up agreement to a sweeping Economic Cooperation Framework Agreement signed in 2010 to reduce trade barriers between China and Taiwan.
Ma has overseen a marked thaw in relations with Beijing since he came to power pledging to strengthen trade and tourism links. He was re-elected in January 2012.
But China still considers Taiwan as part of its territory awaiting reunification -- by force if necessary.