In 1878, Kirby bought out his partners and established the Onohama Shipyards, bringing his brother Alfred from Karachi as engineering director.
In 1882, the company launched Japan's first commercial iron-ribbed steamship, the Dai-ichi Taiko Maru (第一太湖丸), which operated on Lake Biwa.
The success of this venture led to a contract from the Imperial Japanese Navy to construct the second of the Katsuragi-class corvettes, the Yamato.
However, due to problems with financing, and delays in completion of Yamato caused when suppliers in the UK went on strike, Kirby faced foreclosure on a 50,000 Mexican dollar loan from the Hong Kong & Shanghai Bank, and committed suicide in 1883.
After Kirby's death, the company survived under Japanese government receivership, coming under the control of the Kure Naval Arsenal in 1890.