A report from news agency Reuters said that the German shipping line and a number of banks are seeking assurances that Qatar will remain committed to UASC in the long-term.
Two finance sources told the news agency that one of the main concerns of Hapag Lloyd and some of the Gulf-based syndicate banks is that Qatar could in future lower its stake in the combined group.
The apparent worry is that rival container shipping lines could acquire a stake in the merged group if Qatar sells shares, one of the sources said.
The news comes less than two weeks after Hapag-Lloyd postponed the completion date of its takeover from 31 March to 31 May, but insisted the deal was not in doubt.
Hapag Lloyd chief executive Rolf Habben Jansen told a news conference this week he had underestimated the complexity of the EUR7bn - 8bn deal, which will create one of the world's largest shipping lines.
Currently, Qatar holds a 51% stake in UASC, Saudi Arabia has 35% and the rest is owned by United Arab Emirates, Bahrain, Kuwait and Iraq.
Under the terms of the new structure, Qatar will hold 14% in the merged group via QIA's subsidiary Qatar Holding LLC, while Saudi Arabia will have a 10% stake.
Another factor said to be holding up the deal is the proposed sale of shipping company United Arab Chemical Carriers, which is necessary under the terms of the merger.
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