The decision comes as Warsaw is involved in European diplomacy on the political crisis in neighbouring Belarus.
On Wednesday, Czaputowicz received prominent Belarusian opposition activists Valery and Veronika Tsepkalo.
The departure of Czaputowicz, who had been in the post since 2018, follows that of health minister Lukasz Szumowski on Tuesday.
Szumowski, a cardiologist, has been at the centre of the struggle against the novel coronavirus in Poland, where infection rates have been relatively low compared to many countries in western Europe.
Asked about the timing of the departures, Polish Prime Minister Mateusz Morawiecki said “when it comes to politics, I don’t think there’s ever a good time.”
“What if a minister had resigned two months ago, before the first round of the (presidential) election?” he said Thursday.
“Or four months ago when the coronavirus was gathering steam and we had the European Union budget negotiations — there’s never a good time,” he told reporters.
Morawiecki announced the new health minister would be Adam Niedzielski, an economist at the helm of the national health fund since 2019.
As for Poland’s next top diplomat, Morawiecki named Zbigniew Rau, a lawyer and lawmaker who heads the foreign committee in parliament.
Morawiecki said they would take up their new duties in the coming days, adding that their predecessors had given considerable notice before leaving.
Czaputowicz’s office gave no precise reason for his resignation, but told the PAP news agency that “the minister has in the past said the post-election period was the right time for a change” in the post of foreign minister.
President Andrzej Duda was returned to power in a run-off vote last month, backed by the populist
right-wing Law and Justice (PiS) party.
Szumowski cited personal reasons for his departure. But Polish media have accused his ministry of failing to supervise the procurement of items such as face masks during the pandemic.