The price of the deal was not disclosed, local portals total-croatia-news.com and seenews.com report.
The acquisition will be subject to regulatory approvals in several markets, Fortenova said in a statement late on Friday.
Regardless of a possible change in co-ownership, the Fortenova Group continues regular business operations, the statement added.
Fortenova owns Slovenia's largest grocery retailer, Mercator, and Croatia's biggest food retail chain, Konzum.
The stores have a significant combined market share in Bosnia and Herzegovina.
The Indotek Group, owned by Hungarian and American investors, manages assets worth more than EUR 3 billion in total.
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