Kuehne was taking advantage of shares being sold by TUI , which on Tuesday completed the disposal of its remaining 7.9 percent of shares to focus on cruise ship acquisitions.
TUI's move allowed Kuehne to expand its investment in Hapag-Lloyd, which it said it considered to be long-term.
"The ongoing shipping industry consolidation offers Hapag-Lloyd new growth perspectives and strengthens its positions among the most important shipping companies across the world," Kuehne Holding executive chairman Karl Gernandt said.
Kuehne started investing in Hapag-Lloyd in 2008 to support the company's Hamburg base and fend off an approach by Singapore-based shipping rival NOL.
Hapag-Lloyd's biggest shareholders, apart from Kuehne and the city of Hamburg, are Arab peer UASC, which it took over this year, reaching a joint number five position in worldwide shipping.
In 2014, it took over Chilean peer CSAV.
The most recent example of consolidation in shipping, which further boosts the existing group of top companies, is this week's bid by China's COSCO for Hong Kong peer Orient Overseas (OOIL).