The large turnout of protesters, which had reached up to 10,000 people, led Chen, who departs Friday morning, to cancel a news conference he scheduled for Thursday evening.
Differences and challenges
Protesters have been angered by the deals that both governments insist will bring enormous economic benefit to both sides, fearful that money and jobs will flood out of Taiwan to take advantage of the labour and resources of China.
Ma said: "What cannot be denied is that differences and challenges still exist between the two sides, especially on the issues of Taiwan's security and international space.
"I wish in the future when handling disagreements, the two sides may cooperate on the basis of reality, without denying each other, serve the people, and maintain peace across the strait."
Ma is the first Taiwan president to have contact with a top Chinese official on the island.
As expected, however, Chen did not address the Taiwan leader by his formal title, "president".
Tsai Ing-wen, chairwoman of Taiwan's opposition Democratic Progressive Party, had said before the meeting that the issue involved more than manners and political semantics.
"People feel anxious especially when we have to wonder whether the president, Taiwan's democratically elected president, will be addressed as president," she said.
"If he [Ma] cannot even defend his own title, what can he defend for us?"
On Wednesday hundreds anti-China protesters had laid siege to the Grand Formosa Regent Taipei hotel, trapping the Chinese envoy and his delegation inside for several hours.
The protesters tossed eggs, burned Chinese flags, blocked traffic and chanted "communist bandit get out" while he attended a dinner banquet hosted by the ruling Nationalist party.
The demonstrators, who came from various political groups, were concerned over Ma's efforts to seek closer ties with the mainland.
Despite the protests, Chen's visit signals warming times between the two rivals.
For nearly six decades, Taiwan banned direct flights and shipping with China, fearing Beijing might attack with bombers and warships disguised as civilian vessels.
However, the signed agreement plans to increase aviation and shipping links between China and Taiwan. It also includes measures for better cooperation with food safety issues.