SG Holdings bought 586 million shares at 10.70 rupees a share Friday.
Group chief executive Hanif Yusoof said with the entry of the Japanese investor Explanka would become a truly global company.
Founding family members of the group, including Osman Kassim, Sattar Kassim, Shafik Kassim, Farook Kassim and chief executive Yusoof, were among the sellers.
The Japanese group is expected to make an offer to other shareholders which can take its stake above 51 percent.
The 34 year old Expolanka's core business is logistics and it has built up a network spanning 17 countries including South Asia, East Asia and Africa.
Yusoof is expected to continue as chief excutive, the firm said in a stock exchange filing.
Analysts say the interest of a Japanese firm in Sri Lanka is an indication of the island's growing importance as a logistics hub.
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