Czerwinska had expressed skepticism over the government's ability to pay for new social spending programmes earlier this year, according to local media.
It was unclear whether Czerwinska was sacked or had resigned. ING Bank economists wrote in a daily report that her departure could clear the way for a limited broadening of the government's tax cuts for young people.
Other incoming ministers will replace officials who won posts at the European Parliament following last month's election, including powerful interior minister Joachim Brudzinski.
The nationalist Law and Justice government had put forward some of its most senior politicians for the European vote, winning 26 of the 51 seats reserved for Poland.