Police arrived on the scene and immediately arrested the 62-year-old driver of a 1-ton truck that embedded itself in the main embassy gate at around 5 a.m., a report by Yonhap news agency said.
No damage was reported, though the main gate was pushed back several feet, Yonhap said.
"The Korean government expressed regrets to the Japanese Embassy over the incident and will take necessary measures, including tighter security near the embassy," a senior official at Seoul's Foreign Ministry said.
The driver, named Kim, said he smashed into the gates to protest what amounted to an insult by another protester, a Japanese man named Nobuyuki Suzuki.
In December former Korean sex slaves, or comfort women, and their supporters set up a bronze statue of a young girl in front of the Japanese Embassy. The statue is a symbol of defiance against their treatment by Japanese soldiers during the occupation in World War II.
Nobuyuki later posted a video clip on his blog showing him setting up his protest, which read "Dokdo is Japanese territory," a reference to Japan's claim to the disputed islands in the South China Sea.
A group of 10 local women who were comfort women filed a defamation suit with a Seoul prosecutor's office against Nobuyuki earlier this month, Yonhap reported.
Police said Kim rammed the Japanese Embassy gates to protest Nobuyuki's use of the statue, which he said was an insult to Koreans.
Japan reportedly lodged a formal diplomatic protest about the incident and requested tighter security.
The Dokdo Islands are in reality a group of two main islets rising to nearly 560 feet and surrounded by dozens of sharp rocks protruding from the sea. They are sometimes called the Liancourt Rocks and known by the Japanese as Takeshima.
The volcanic rock islands are 46 acres in area and are slightly closer to mainland South Korea, around 135 miles, than Japan, 155 miles. The nearest land mass is Korea's Ulleung-do Island at about 55 miles away.
Like many disputed islands in the South China Sea they have little use as an inhabitable area and offer some appeal as an ecological point of interest.
Their real value lies in the accompanying ownership of the surrounding sea because of fish resources as well as oil and gas deposits on the seabed.