Japanese Defence Minister Itsunori Onodera said the incident happened on 30 January near islands claimed by both nations in the East China Sea.
He said this had prompted Tokyo to lodge a formal protest with Beijing.
The row, over islands known as Senkaku in Japan and Diaoyu in China, has escalated in recent months.
Taiwan also claims the island chain (known as Diaoyutai in Taipei), which is controlled by Japan.
Last week, tensions between Tokyo and Beijing appeared to be easing after a Japanese delegation met senior Chinese leaders and both sides later expressed hopes that relations could improve, the BBC's Rupert Wingfield-Hayes in Tokyo reports.
But on Monday China sent patrol ships back in to the disputed waters around the islands, our correspondent adds.
'Dangerous situation'
"On 30 January, something like fire-control radar was directed at a Japan Self-Defence Maritime escort ship in the East China Sea," Mr Onodera told reporters on Tuesday.
The minister said Japan's Yuudachi vessel and the Chinese frigate were about 3km (one mile) apart at the time, Japan's Kyodo News reports.
Asked about the delay in filing the protest, Mr Onodera said it took the ministry until Tuesday to determine that a fire-control radar had indeed locked on the Japanese ship.
He added that a Japanese military helicopter was also targeted with a similar type of radar by another Chinese frigate on 19 January.
"Directing such radar is very abnormal. We recognise it would create a very dangerous situation if a single misstep occurred," he said.
Radars use radio waves to detect the intended target and then guide missiles or other weapons.
China's UN move
Also on Tuesday, the Chinese ambassador to Japan rebuffed an earlier protest over continuing Chinese patrols off the disputed islands, according to China's state-run Xinhua news agency.
Ambassador Cheng Yonghua said the islands and the surrounding waters were China's "inherent territory".
The dispute over their ownership of the islands has continued for years, but it reignited in 2012 when the Japanese government purchased three of the islands from their private Japanese owner.
The move triggered diplomatic protests from Beijing and Taipei, and sparked small public protests in China, affecting some Japanese businesses operating in the country.
Chinese government ships have since sailed many times through what Japan says are its territorial waters around the islands.
Late last year, a Chinese government plane also flew over the islands in what Japan called a violation of its airspace.
In response, Tokyo has moved to increase military spending for the first time in a decade.
The eight uninhabited islands and rocks lie close to strategically important shipping lanes, offer rich fishing grounds and are thought to contain oil deposits.
In December, Beijing submitted to the UN a detailed explanation of its claims to the disputed islands.
A UN commission of geological experts will examine China's submission but does not have the authority to resolve conflicting claims.-British Broadcasting Corporation (February 05, 201312:21 GMT)
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