The properties used to house the St Monica’s Hospice and were purchased by property developers Blok.
Earlier on Thursday, the Western Cape High Court ordered Blok to put construction in the Bo-Kaap on hold, prohibiting its crane from entering the area until a next court date is determined.
Residents have been fighting developers, accusing them of stripping the historical area of its culture and heritage.
Two weeks ago chaos erupted as residents and police clashed during a protest.
The Western Cape National Heritage Council confirmed last week that it has received an application to declare Bo-Kaap a heritage site.
And the City’s mayoral committee this week resolved to support the designation of the Bo-Kaap as a Heritage Protection Overlay Zone (HPOZ).
Following court proceedings on Thursday, Loonat and residents headed to the police station.
“We believe there is some collusion and a corrupt relationship between the parties involved in this matter and have opened a criminal case which includes conspiracy to commit fraud and theft, the contravention of the Finance Management Act and under the Prevention of Combating Crime Act.
“There is corruption and Bo-Kaap’s residents are suffering,” Loonat said.
Police spokesperson Warrant Officer Joseph Swartbooi confirmed: “A fraud case was opened at Cape Town Central Police for further investigation.”
City spokeswoman Priya Reddy said: “The City will consider representations on this matter.”