DRC President Felix Tshisekedi had summoned five ministers who are members of Katumbi's Ensemble pour la Republique (Together for the Republic) party to "know their position" on Wednesday, his office said.
The minister of planning, the minister of transport and the vice-minister of health tendered their resignations later, the presidency said.
Tshisekedi, who came to power in January 2019, has already announced that he intends to run for a second term next year.
DRC's economy has been battered by the COVID-19 pandemic and the Ukraine war since Tshisekedi was first elected in 2019, hiking inflation and the cost of living in the mineral-rich country.
Martin Fayulu, the second-place finisher in the last presidential vote, has already announced his intention to run against Tshisekedi again.