Trump acted quickly, just a day after Perry told the president he would be stepping down by the end of the year.
Last week, the chairmen of the House Intelligence, Oversight and Foreign Affairs committees subpoenaed Perry to provide documents related to his role in USA energy policy in Ukraine and whether he was involved in decisions to withhold military aid.
Perry faces a Friday deadline to comply with a House subpoena regarding information about Ukraine.
".@SecretaryPerry is a good man & good friend who has devoted his life to serving his country & the great state of Texas".
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House investigators have subpoenaed Perry for documents related to Trump's call with Zelensky, which has triggered an impeachment inquiry into whether the president abused his power when he asked Zelensky to investigate former vice president Joe Biden, a political opponent, and his son Hunter. But since then, the White House has defied those requests because it regards the impeachment inquiry as illegitimate without an official House vote.
Most recently, Perry told eventgoers at a news conference in Vilnius, Lithuania, that he had no intention to depart from the Trump administration. Biden never came up in any discussions Perry had with Zelenskiy or the White House, he said.
He has travelled from Japan to former Soviet states to Qatar, Israel and beyond, promoting US natural gas and production companies.
The administration has been working to get Ukraine back into the "sphere of influence of the United States", said Perry, and that meant to get rid of corruption in Ukraine. "I know Rick has been with me three years, he's right here. I endorsed him for President in 2008", he said on Fox News.
The announcement confirmed recent press reports that Perry would be stepping down in the near future.
Word of Perry's resignation came as Trump traveled to Texas for a rally on Thursday evening.