Kadry has been one of the key negotiators in the much-delayed IMF negotiations to obtain the loan package.
"The only comment I can make for the time being is that, yes, my term ends on April 30 according to my resignation, which I submitted in December," Kadry said.
"My next move is not decided."
Analysts believe that his resignation could jeopardise Egypt's chances of receiving the IMF loan early.
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Kadry joined the Ministry of Finance in July 2004 as a senior advisor and director of the Macro Fiscal Unit at the minister's office. He was appointed as a deputy minister in March 2007.
Since the ousting of former president Hosni Mubarak in 2011, Kadry survived the change of five finance ministers in office.
Egyptian daily Al-Watan reported that Kadry resigned because of pressure put on him by the Freedom and Justice Party (FJP) and that he had clashed with FJP advisor to the minister of finance Abdallah Shehata.