Bakers say escalating production costs have made the government-imposed price of a loaf unviable.
The bread sections in many stores in Harare's surburbs were empty while others had only a few loaves in stock.
It follows a police crackdown on bakers and retailers who had increased the price of bread without state approval.
On Saturday, many defied the government by raising the price of a standard loaf from the official Z$200 (A$1.10) to Z$330 (A$1.80).
In response, police were deployed across Harare and on Sunday a director of a leading baker was arrested for flouting price controls.
Police said they would continue to enforce the price regulations on bread.
"We are still monitoring the situation and our surveillance teams will remain on the ground to ensure the law is followed… “ police spokesman Andrew Phiri told AFP.
The bakers' association said last week that the cost of a loaf of bread should be increased to protect bakers against spiraling production costs.
"Over the last two months the baking industry has been overwhelmed by substantial increases in input costs to the point where viability, at current prices, is seriously threatened," the association said.
"It is crucial to keep the industry going and also retain approximately 20,000 jobs in the industry."
Zimbabwe introduced price controls four years ago.
The measures were aimed at fighting a burgeoning black market in staples such as cornmeal, cooking oil and bread.
Violators face fines of up to one million Zimbabwean dollars (A$5,509).