The raids took place Wednesday in the cities of Warsaw, Gdansk, Lodz and Zielona Gora. They targeted two organizations, the Women's Rights Center and Baba, which help victims of domestic violence and which also participated in this week's anti-government protests.
Women's rights activists said Thursday the loss of files would hamper their work, and accused authorities of trying to intimidate them. Prosecutors denied the accusation, saying the timing of the raids a day after the women's marches was purely coincidental.
Some fear the ruling Law and Justice party, led by Jaroslaw Kaczynski, is following in the footsteps of neighboring Hungary, where non-governmental groups have faced harassment under Prime Minister Viktor Orban.
"This is an abuse of power because even if there is any suspicion of wrongdoing, an inquiry could be done in a way that doesn't affect the organizations' work," Marta Lempart, the head of the Polish Women's Strike, which organized this week's street protests, told The Associated Press.
The women's groups said they were told by police that prosecutors were looking for evidence in an investigation into suspected wrongdoing in the Justice Ministry under the former government. At the time the Justice Ministry provided funding to the women's groups.
"We are afraid that this is just a pretext or warning signal to not engage in activities not in line with the ruling party," The Women's Rights Center said in a statement. Anita Kucharska-Dziedzic, who heads the group Baba, said police entered her office in Zielona Gora, western Poland, on Wednesday at 9 a.m. (0700 GMT) and worked until 6 p.m. removing files.
She told the AP her group has never been aware of any wrongdoing by Justice Ministry officials that her group was in contact with. She also said she now expects to have problems continuing her projects due to the loss of files, and is also concerned because the documents contained private information on domestic abuse victims who have sought the group's help.
Barbora Cernusakova, Amnesty International's researcher on Poland, called the police operations "very worrying." "We understand that the police actions came in the context of an investigation against former staff of the Ministry of Justice, but the NGOs, and the women and girls they support, will suffer the consequences," Cernusakova said.
Jacek Pawlak, a spokesman for prosecutors in Poznan, where the investigation is being led, said the raids were part of an ongoing investigation but would not divulge what the probe was about. He said there was no attempt to harass the women's organizations.
This week's street demonstrations came on the first anniversary of a mass "Black Protest" by women dressed in black that stopped a plan in parliament for a total ban on abortion. Despite that success the women's rights activists marched to protests the fact that abortion is still illegal in most cases, calling for a liberalization of the law.
Monika Scislowska in Warsaw contributed to this report.