Gontareva, who has been in her post since 2014 and oversaw tough anti-crisis measures, will give a news conference at 1100 (0800 GMT).
"Yes, it's true, she has submitted (her resignation)," the official said, confirming an earlier report by Russian media, Reuters reported.
A former investment banker and business partner of President Petro Poroshenko, Gontareva took charge nearly three years ago after Russia's annexation of Crimea and with the country in the throes of a pro-Russian separatist uprising.
She introduced sweeping reforms, including shutting down half the country's lenders and switching Ukraine to a flexible exchange rate.
Her measures won praise from the International Monetary Fund, which has supported the country with a $17.5 billion bailout since 2015, but were criticized by protesters and some lawmakers.