She told public broadcaster Polish Radio that Czaputowicz's decision came after he indicated earlier this year that he would resign to make room for a new face.
"The minister previously stated that the time after the presidential election would be a good time to make the change and expressed his hope that his successor would continue the current line of policy and work to further strengthen Poland's position in the international arena," Szatyńska-Luft said.
Czaputowicz took over as Poland’s foreign minister in January 2018 to replace Witold Waszczykowski in a sweeping government reshuffle.
He previously served as a deputy foreign minister.
Czaputowicz began working at the Polish foreign ministry in 1990. He was deputy director and then director of the ministry’s Consular and Emigration Department from 1990 to 1992. From 1998 to 2006, he was deputy head of the Civil Service.
From 2006 to 2008, he headed the ministry’s Department of Strategy and Foreign Policy Planning. From 2008 to 2012, he managed the National School of Public Administration (KSAP).
A political scientist, Czaputowicz has written more than 100 articles and books focusing on topics such as international relations, security and sovereignty, according to the Polish foreign ministry.
His resignation comes after Health Minister Łukasz Szumowski, who has been at the centre of Poland’s battle against the COVID-19 epidemic, announced on Tuesday he was quitting.
The country's conservative leader Jarosław Kaczyński said earlier this month that Poland's government would undergo a reshuffle by the end of September or in early October at the latest.
Kaczyński, who heads Poland’s ruling conservative Law and Justice (PiS) party, did not name any Cabinet ministers who could be replaced.
Kaczyński has previously said that Prime Minister Mateusz Morawiecki will keep his job as head of government.
New Polish FM to be announced 'shortly'
Meanwhile, Morawiecki’s top aide, Michał Dworczyk, said on Thursday that the prime minister accepted Czaputowicz’s resignation and “thanked him for his work.”
A new Polish foreign minister will be announced “shortly, together with a new health minister,” Dworczyk said on Twitter.
Officials have previously said that the name of the new health minister would be announced by the end of this week.