Goncharuk had offered to quit in January after a leaked recording emerged of him questioning President Volodymyr Zelensky's grasp of economics, only for the head of state to refuse his resignation.
Although government officials did not confirm that Goncharuk was stepping down, MPs from Zelensky's party said his departure was announced during a meeting with the president and that a parlimentary vote to approve it would be held on Wednesday.
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Zelensky planned to replace his 35-year-old prime minister -- the youngest premier in Ukraine's history -- because he was unhappy with the government's performance on economic issues, official sources told AFP last week.
Goncharuk denied having presented his resignation on Monday but admitted "consultations on the subject" had taken place with the president.
However, late on Tuesday, MPs from the president's Servant of the People party were told of his resignation during a meeting with Zelensky, parliamentary deputy Ievgenia Kravtchuk told AFP.
Zelensky told party members that Denys Chmygal, one of the vice-premiers, would take up the reins of government, Kravtchuk said.
The news was confirmed by two of her parliamentary colleagues -- who said the foreign, finance and defence ministers would also be replaced.
Goncharuk had been nominated for the post by Zelensky last August against the backdrop of a struggling economy and a protracted war with Russian-backed separatists in the east.
But since the president's refusal to accept his last resignation, Zelensky's party has criticised the work of his government.
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Comedian-turned-politician Zelensky came to power last April promising to "break the system" that had ruled Ukraine since independence in 1991.
Among his campaign promises were ending the conflict in the east, fighting corruption and launching economic reforms in one of Europe's poorest countries.
His party won legislative elections in July and formed a government including a number of inexperienced ministers.
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