Tens of thousands of demonstrators – many of them young – took to the streets in days protesting against Merino following the ouster of his predecessor Martin Vizcarra, 57, who was impeached on corruption allegations on Monday.
They accused Congress of staging a parliamentary coup against Vizcarra, who enjoyed continued support among many voters for his attempts at reform.
Congress’ ultimatum came after the health ministry said two protesters were killed on Saturday during a massive and peaceful march in Lima, which was repressed by police firing shotgun pellets and tear gas.
Police reportedly fired tear gas and shotgun pellets to repel demonstrators, some of whom had thrown fireworks and stones.
Two men, one aged 24 and the other 25, were killed. Medical officials said they had died from gunshot wounds.
Following this, twelve ministers from his recently-appointed cabinet resigned earlier on Sunday, all in protest against police brutality and Merino’s manner of handling of the protest.
Merino had been expected to retain the presidency until July 2021 – when Vizcarra‘s term was due to end.
Vizcarra has been embroiled in a bitter battle with Congress, which is dominated by rival parties, since he took office in March 2018.
He has denied allegations that he accepted bribes worth 2.3m soles ($640,000; £487,000) when he was governor of the southern Moquegua region.
Merino’s resignation was greeted by noisy celebrations in the country’s capital, Lima, with demonstrators taking to the streets sounding horns and banging pots.