The mayor of Warsaw ordered the dismissal of Bogdan Chazan, a city hall spokesman said today, after the doctor invoked his Catholic faith to refuse to carry out the procedure.
"A doctor can refuse to carry out an abortion on moral grounds, but a public hospital cannot," said spokesman Bartosz Milczarczyk.
The woman was referred to another public hospital, but by that point she was five days past the legal 24-week abortion limit.
Staunchly-Catholic Poland allows abortion up to 12 weeks of pregnancy in cases of rape or incest, or 24 weeks in cases of irreversible foetal malformation or a threat to the mother's life.
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After that point the procedure can be allowed on a case-by-case basis if the mother's life is at risk.
State prosecutors in the Polish capital have opened an investigation into the woman's case, while her lawyer is seeking damages from the hospital.
The doctor's dismissal has polarised debate between pro- and anti-abortion camps in the overwhelmingly Catholic country whose abortion laws are among the most restrictive in Europe.
Cardinal-Archbishop of Warsaw Kazimierz Nycz dubbed Kazan's dismissal "a dangerous precedent", breaching constitutional guarantees for freedom of conscience.
"Lawmakers cannot make doctors act against their conscience," he told reporters.
But Wanda Nowicka, deputy speaker of parliament and a top women's rights advocate, believes the Kazan case has set a different kind of precedent.
"This isn't the first time a woman was refused her right to a legal abortion... But this time the state decided not to sweep it under the rug and is dealing with it," Nowicka said.
Women's rights groups have hailed city hall's decision to dismiss Kazan as both legal and appropriate.
"There's no joy among women's rights groups over this decision, which simply upholds the law," Krystyna Kacpura, head of the Polish Federation for Women and Family Planning said.