Under Japanese law, female imperial family members forfeit their status upon marriage to a “commoner” although male members do not.
She also skipped the usual rites of a royal wedding and turned down a payment offered to royal females upon their departure from the family.
She is the first female member of the royal family to decline both.
The couple are expected to move to the US – where Mr Komuro works as a lawyer – after marriage. The move has drawn inevitable comparisons with British royals Meghan Markle and Prince Harry, earning the newlyweds the nickname “Japan’s Harry and Meghan”.
Like Ms Markle, Mr Komuro has come under intense scrutiny since his relationship with Ms Mako was announced. He was most recently criticised for sporting a ponytail when he returned to Japan.
“I am very sorry for the inconvenience caused and I am grateful for those… who have continued to support me,” she said, according to an NHK report. “For me, Kei is irreplaceable – marriage was a necessary choice for us.”
Mr Komuro added that he loved Ms Mako and wanted to spend his life with her.
Princess Mako left her Tokyo residence at around 10:00 local time on Tuesday (01:00 GMT) to register her marriage, bowing several times to her parents, Crown Prince Fumihito and Crown Princess Kiko. She also hugged her younger sister before she left, news outlet Kyodo reported.
There has been excessive media coverage around the couple over the years, which has caused the princess to suffer from post-traumatic stress disorder, the Imperial Household Agency (IHA) had earlier said.
Her relationship has been met with controversy in the country.
On Tuesday, people were pictured protesting against the marriage in a Japanese park.
Many slogans appeared to bring up financial issues around Mr Komuro’s family – specifically his mother.
The reaction to Princess Mako and Kei Komuro’s relationship by some media and people in Japan, has highlighted the pressure women in Japan’s imperial family face.
The Imperial Household Agency has said Princess Mako suffered from post-traumatic stress disorder because of the harsh criticism from the media and on social media around her engagement since it was announced nearly four years ago.
She is not the first woman in the Japanese royal family to be affected this way.
Her grandmother Empress Emerita Michiko temporarily lost her voice nearly 20 years ago when criticised by the media as being somehow unfit to be the Emperor’s wife. Her aunt-in-law Empress Masako, suffered depression after she was blamed for failing to produce a male heir.
Royal women have been forced to strictly adhere to certain expectations – they must be supportive of their husbands, produce an heir, and be a guardian of Japan’s traditions. If they fall short they are savagely criticised.
This is also true of Princess Mako, who said she would give up her royal status. But even that has not been enough to stop the attacks on her, her husband, and their marriage.