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The EU was retroactive, inconsistent on Apple-Ireland deal, Cramer says

CNBC's Jim Cramer said Tuesday that the European Union was retroactive when it ordered Ireland to recoup millions in taxes from Apple.

The European Commission on Tuesday told the Irish government to retrieve about 13 billion euros ($14.5 billion) in taxes from Apple, after regulators said Ireland granted Apple undue tax benefits.

"A deal's a deal," Cramer said on "Squawk on the Street. "The Irish wanted to give it away. They took it."

Cramer was critical saying the EU shouldn't expect Ireland, as a sovereign state, to "check-in" on its deal.

"If I were the EU, I would say, 'Listen, from now on, every single deal has to be run through us,'" Cramer said."... But to do retroactive is a little difficult. We've often criticized our government when they do something retroactive."

Additionally, Cramer said companies with deals similar to Apple's could be worried. The ruling also may impact Ireland's ability to attract other investments from global companies. The EU will continue to investigate Amazon and McDonald's European tax affairs, according to EU Commissioner Margrethe Vestager.

Apple's stock was trading slightly lower at $106.20 Tuesday afternoon.