"Vladimir Putin has published a decree relieving Ulyukayev of his functions," Peskov said, adding that the president had "lost confidence" in the minister.
Ulyukayev had earlier been placed under house arrest for two months over suspicions he pocketed a two-million-dollar payoff during a deal involving state-controlled oil giant Rosneft.
Ulyukayev was the highest ranking official detained over suspected corruption since President Vladimir Putin took power in 2000 and his arrest sparked speculation over whether the probe is linked to an internal power struggle.
Investigators accused Ulyukayev of "threatening (and) using his ministerial powers to create obstacles to the company's activities in the future".