China claims self-ruled Taiwan as part of its territory, and relations between the two have soured in recent years.
Last week two Chinese crew members died after a boat capsized near Kinmen, an island administered by Taipei but located just five kilometres from the mainland city of Xiamen.
It was being pursued by Taiwan's coast guard for being within prohibited waters.
Taiwan's Premier Chen Chien-jen said Tuesday that both sides had been aware of "restricted and off-limits sea areas" since 1992.
"We will continue to protect these sea areas to ensure safety in our territorial waters and the rights of our fishermen," he told reporters outside Taiwan's parliament.
"We hope both sides can be rational, equitable and cooperate with each other to ensure the safety of the Kinmen-Xiamen waters so that the people from both sides of the strait can engage with each other in a healthy and orderly manner."
Taiwan's defence minister said the military would not get involved, leaving it to the coast guard to monitor waters around Kinmen, "because we want to avoid war".
"If we intervene, it will escalate the conflict which we do not want to see," Chiu Kuo-cheng told reporters.
"Let's handle the matter peacefully."
Beijing has never renounced the use of force to bring Taiwan under its control, and in recent years has ramped up the rhetoric of "unification".
It has stepped up military pressure on Taiwan by deploying warplanes and naval vessels around the island on a near-daily basis.
Last month Taiwan had a presidential election which ended in a win for the Democratic Progressive Party's Lai Ching-te -- a candidate Beijing considers a "separatist".
Taiwan's defence ministry on Tuesday said it detected 24 Chinese warplanes around the island in the 24 hours to 6 am -- a slight uptick compared with recent days.
- 'Strong indignation' -
Relatives of the two deceased crew arrived in Kinmen on Tuesday, accompanied by representatives of the Red Cross Society of China.
Li Zhaohui, a Red Cross representative, told reporters that the "vicious incident caused strong indignation in China".
"The purpose of our trip to Kinmen is to understand the truth, assist the family members in the aftermath, and bring back the two survivors," he said.
The families are expected to take part in religious rituals mourning the deceased, who will be cremated, and they will stay in Kinmen until Wednesday.
China had condemned the incident, with Zhu Fenglian, spokesperson of Beijing's Taiwan Affairs Office, saying Monday Taipei should facilitate the relatives' visit to "avoid further hurting the feelings of compatriots on both sides of" the strait.
Taiwan's coast guard had defended its actions during the pursuit that led to the deadly capsizing, saying the Chinese crew refused to cooperate with law enforcement.
It is not uncommon for Chinese and Taiwanese ships to accidentally enter the other's side.
After last week's fatal incident China announced stepped-up patrols around Taiwan's waters, and on Monday members of its coast guard briefly boarded a Taiwanese cruise ship to check the captain and passengers' details.
Kinmen legislator Chen Yu-jen said the tourist ship had sailed "about one kilometre" into mainland waters.
"When relations between the two sides were relatively peaceful, we would not board each other's boats... It's because at that time there was a tacit understanding and the two sides would not take tougher actions," she told reporters.
But now with tenser cross-strait relations, she urged Taiwan's tourist boats and fishermen to stay within their waters.
"This is the safest way," Chen told reporters.
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