Civil Liberties Minister Helena Dalli said that a person should not cover his/her face in public if this will make others feel unsafe. She also pointed out that in an open society people should not cover their face.
Speaking at a party rally in Birzebbuga, she said the existing law made it clear that people could not wear a mask or change their appearance in a public place.
"My right to dress as I please stops when it impinges on another person's right to enjoy security," Dr Dalli said, adding the government was considering changing the law to make it "clearer".
She said that the issue is not about a religion or other and nobody should take any offence.
The minister's words came after PN MP Jason Azzopardi had said Maltese law demands visual recognition, so wearing a burqa must be prohibited.
Writing on Facebook earlier, she said it was a PN administration that directed Police not to enforce the law on burqas, and that Dr Azzopardi formed part of the cabinet when this happened.
The debate on whether individuals should be allowed to wear burqas is attracting public interest, with some saying such persons should be left to do as they please while others are calling for a burqa ban for "safety and security reasons".
Article 338 of the Criminal Code states that it is a contravention against public order if anyone "in any public place, wears any mask, or disguises himself, except at the time and in the manner allowed by law".
This is punishable with up to two months' detention, as for any other contravention.
Dr Dalli said: "We should be allowed to enjoy our rights as long as these rights don't prevent others from enjoying theirs.
Dr Dalli highlighted that the law should be clearer so as to avoid any misinterpretations.
The minister also posted a link to a European Court of Human Rights ruling on burqas published in Britain's The Guardian in July 2014 after ECHR judges upheld France's burqa ban, accepting Paris's argument that it encouraged citizens to "live together".
The case had been filed by an unnamed 24-year-old French citizen of Pakistani origin, who wears both the burqa, covering her entire head and body, and the niqab, leaving only her eyes uncovered.
The law, introduced in 2010, made it illegal for anyone to cover their face in a public place. While it also covers balaclavas and hoods, the ban has been criticised as targeting Muslim women.
The French government asked the court to throw out the case, claiming that the law was not aimed at the burqa or veil but any covering of the face in a public place, and also applied to hoods and helmets when not worn on a motor vehicle.
The minister said that the government is working to help integrate all those people who want to live in Malta.