At least 20 of the migrants, who claim to be from central Africa, are feared dead. The boat was found in distress, the newspaper says, and the migrants appeared to have been at sea for many days.
Along with southern Italy, Malta is one of the main points of arrival for migrants attempting the crossing from North Africa into Europe, Reuters reports.
Their point of departure has not yet been established.
The rescue is the first in several months, the Times of Malta reports. It comes at a time when the number of migrants in detention has slipped to a low of just 29. At one time there were over 2,000.
According to Reuters, an Italian coastguard vessel picked up a separate boat carrying around 70 migrants off the coast of Libya on Thursday.
Arrivals from North Africa have slowed in recent months with more coming on larger cargo ships from Syria, the agency says.