Police spokesman, Joseph Sauka said "Windows at a mosque and the local priest's home were smashed and three people were hurt during the incident."
Clashes between members of the Anglican church and Muslims broke out last Monday following reports that young men, reportedly from the church snatched hijabs off the heads of pupils on their way to school in M'manga, about 100 kilometres from the city of Blantyre.
Classes were suspended at three primary schools and a public secondary school in the area after the church disagreed that girls could wear the hijab to school.
Parish priest Mphatso Bango said that when the Anglican church constructed the schools and gave them to the government, a set uniform was agreed on.
However, the national taskforce on Hijab spokesman Abdul Fadweck said they and the church had agreed over the weekend that Muslim girls could wear the headscarf until a long-term solution is found to the uniform compliance.
Principal secretary for the education ministry, Justin Saidi, said in a statement that while generally there are no conditions attached to the handover of these schools to government, they had referred the "important" matter to a special committee.
United Nations resident coordinator, Maria Jose Torres said Malawians should "respect each other’s religious beliefs and engage in peaceful dialogue to resolve as intolerance could discourage girls education."