China claims Taiwan as part of its territory and has said it will not rule out using force to bring the island under Beijing's control.
The Chinese military presence around the island announced by Taipei, which included another 23 warplanes and five naval vessels in the 24 hours leading up to 6 am, also came a day after a US warship sailed through the sensitive Taiwan Strait.
The Coast Guard in Taipei said late on Thursday it had detected 12 Chinese ships around its outlying island of Kinmen.
Kinmen, administered by Taipei but located five kilometres (three miles) from the Chinese city of Xiamen, has seen heightened tensions in recent months, with Chinese coast guard ships maintaining a presence around it.
The Taiwan Coast Guard said a fleet of seven ships "belonging to China's maritime and fishery departments entered our restricted waters" around 3 pm local time (0700 GMT), about 4 nautical miles southwest of Kinmen.
"We suspected the fleet, together with three Chinese fishing, boats, were engaged in maritime exercises," it said.
Around the same time, "another fleet of four Chinese coast guard ships entered our prohibited and restricted waters... and another ship sailed outside our waters."
The vessels left about 90 minutes later, the coast guard said, noting that this was "the fourth formation of Chinese coast guard ships sailing in Kinmen waters" in May.
It was also the first time that Chinese coast guard ships "and other Chinese official ships" had sailed together at the same time, it said.
"This has seriously undermined cross-strait peace, stability and navigation safety, hurt the feelings of people on both sides of the strait, and is unhelpful for peaceful exchanges across the Taiwan Strait," the coast guard said.
China has stepped up patrols around Kinmen after a series of deadly fishing incidents earlier this year.
A Chinese speedboat carrying four people capsized near Kinmen on February 14 while Taiwan's coast guard was pursuing it, killing two people.
Another Chinese boat capsized in the area in March, also resulting in the deaths of two crew members.
Taiwan's coast guard had defended its actions but the row has added to tensions, already high after Taiwan's elections in January won by Vice President Lai Ching-te.
Lai, like outgoing President Tsai Ing-wen, rejects China's claim on Taiwan.
- Warship sail-through -
Thursday's maritime presence around Kinmen came after Taiwan's defence ministry said it had detected nearly two dozen Chinese warplanes and five navy ships around the island in the 24 hours leading up to 6 am Thursday (2200 GMT).
That coincided with a US warship sailing through the Taiwan Strait, a narrow 180-kilometre (110-mile) body of water separating the island from China, on Wednesday.
The USS Halsey destroyer "conducted a routine Taiwan Strait transit on May 8 through waters where high-seas freedoms of navigation and overflight apply in accordance with international law", the US 7th fleet said.
It said the Halsey's transit "demonstrates the United States' commitment to upholding freedom of navigation for all nations as a principle".
Chinese naval colonel Li Xi, spokesman for the Eastern Theatre Command, called the US warship sail-through "public hype".
He added in a statement late on Wednesday that the Eastern Theatre command had also organised naval and air forces "to monitor the passage of the US ship through the entire process".
"Troops in the theatre remain on high alert at all times and resolutely safeguard national sovereignty and security," the statement said.
China had warned before Taiwan's elections that Lai would bring "war and decline" to the island, making the lead-up to his May 20 inauguration a closely watched period.
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