The Muslim Brotherhood's activities were banned in 2013 after the army ousted President Mohamed Mursi of the Brotherhood following mass protests against his rule.
The government formed a committee shortly thereafter to manage the Brotherhood's funds and properties. It has since seized the assets of many of the group's leaders.
Egypt sentences journalist union head to two years' jail
Mostafa Sakr, chairman of Business News - the parent company of Al-Borsa, a widely read financial newspaper, and Daily News Egypt, a popular English-language paper - denied any connection to the organisation.
"Our notebooks are open and our assets are clear and they have just one source, our advertisements and subscriptions," Sakr told Reuters.
Egypt court overturns life sentence against ex-president Mursi
"We did not receive any explanations or even warnings about this beforehand whatsoever, so we are extremely surprised by this decision," he said.
Human rights groups have accused Egyptian authorities of widespread violations that include rolling back press freedoms won in the 2011 uprising that toppled veteran autocrat Hosni Mubarak.
Sakr said the company has appealed the committee's decision and that the newspapers will continue to operate as usual.
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