“There has not been any approval by me or the government to hold any pregnancy listing,” Adam Niedzielski wrote on Health Ministry social media on Saturday.
His statement came as some Polish media including Gazeta Wyborcza, Rzeczpospolita or TVN24 reported earlier in the day that a “pregnancy register” was set to become effective as of October 1.
In his tweet, Niedzielski also appealed to the media and politicians not to “sow unnecessary confusion", arguing that the health ministry is "acting here in the interests of patients and for their well-being in line with EU standards.”
In June Niedzielski signed a regulation under which doctors must now record information about pregnancies, including any past or current illnesses, medical visits, treatments and blood type.
The opposition has labelled the medical data list as a "pregnancy register" and an infringement of women's rights.
As Poland has placed a near-total ban on abortion, activists are concerned that women will face unprecedented surveillance from the ruling conservatists.
The Polish government argues the public health data follow EU recommendations and will allow medical workers to help patients both in Poland and abroad.
However, opposition lawmakers say the register could be a "new tool of repression" against women that was aimed to detect possible illegal abortions.
The data can also be accessed by the prosecutor's office, subject to a court ruling, according to media reports.