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6 year oldPresident Donald Trump said Mr Pruitt had done "an outstanding job, and I will always be thankful to him".
But Mr Pruitt has been embroiled in allegations of ethics violations for months.
His deputy Andrew Wheeler will take over as acting head of the agency, Mr Trump said.
The long list of Scott Pruitt controversiesNewer articles
<p>The two leaders have discussed the Ukraine conflict, with the German chancellor calling on Moscow to hold peace talks with Kiev</p>