The attack took place in Mölndal Hospital, where the perpetrator(s) ripped the Holy Quran and spilled drinks on the carpets, a statement by the Gothenburg Mosque Association said.
"Muslims feel offended and hurt in the aftermath of this attack," the statement read, adding that the prayer room allowed Muslims receiving medical treatment at the hospital to receive psychological support and pray.
"The fact that the perpetrators damaged a room where patients receive psychological support shows how much hatred these people have," the statement said, according to the Daily Sabah.
Police reportedly launched an investigation into the matter and have started to examine security footage.
Last September, a mosque in the southern Swedish city of Orebro was burned to the ground in an arson attack. In December, an Islamic Cultural Center in the southern city of Saffle was the target of a homemade bomb attack.
Sweden is a strong draw for many migrants and about 15 percent of its population was born abroad. An estimated 100,000 Turks live in the Nordic country.