Abromavicius had tried to remove figures tied to vested interests from state corporations that have been bleeding money due to suspected corruption and complex offshore schemes.
"I expected this," Abromavicius told the Novoye Vremya weekly's website just hours after his decision to quit.
"But I expected this to come from the old interests (of ousted Russian-backed president Viktor Yanukovych) and not the new ones," he added.
"It came as a big surprise when certain new politicians tried to get their hand on state companies."
Kononenko himself denied the charges and said he was ready to step down from his senior post in Poroshenko's parliamentary faction if his fellow deputies do not trust his work.
But some political analysts said the entire scandal had already undermined Ukraine's reputation and threatened the disbursement of essential assistance tentatively promised by Ukraine's Western allies and the International Monetary Fund.
"Regardless of whether Abromavicius stays or goes, this domestic political crisis is likely to have major repercussions," Anders Aslund of the US-based Atlantic Council wrote in a report.
"The confidence of Western governments in the current Ukrainian administration is running low," Aslund added.
"The International Monetary Fund, the United States, and the European Union had been expected to provide a total of $4 billion (3.6 billion euros) in credits later this month, but none are likely to contribute unless the Ukrainian government shows real commitment to fight corruption." (afp/ez)
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