An affiliate of Warren Buffet’s Berkshire Hathaway Inc. said Monday that it has taken stakes in five of Japan’s biggest trading companies, which have significant oil and natural gas holdings worldwide. 

Subsidiary National Indemnity Company has acquired more than 5% of the outstanding shares of Itochu Corp., Marubeni Corp., Mitsubishi Corp., Mitsui & Co. and Sumitomo Corp. in an investment valued at more than $6 billion. The firm said stakes were acquired over the last year through regular purchases on the Tokyo Stock Exchange. 

Berkshire, which has held interests in businesses such as Coca-Cola Co. and American Express Co. for decades, said in a statement that it intends to hold the Japanese investments for the long term. Depending on price, the firm said it could increase...