The non-profit organization says the break-ins happened Aug. 10 at its Nairn Avenue construction site and Aug. 17 at its site on Riverton Avenue.
In the first case, the suspects took 18 DeWalt cordless drills from one of two trailers they broke into.
The second break-in was more serious as the thieves cleared out a secured construction trailer, taking generators, a Bosch mitre saw, Paslode nailers, a DeWalt reciprocating saw and various other items, according to officials.
Habitat for Humanity Manitoba CEO Sandy Hopkins says the value of the stolen items ranges between $5,000 and $6,000.
The tools are used by volunteers to build Habitat homes, said Hopkins, who added that it's hard to believe someone would steal from a charity that helps low-income people.
"It is very annoying. Very frustrating," Hopkins told CBC News on Monday.
"We work hard in the community to be able to acquire these kinds of tools and use them for many years. And now we will have to dip into fundraising dollars to replace them, and that kind of stuff drives us crazy."
The organization says volunteers were not able to build on Monday morning because of the missing tools, creating a delay in their build schedule.
Habitat for Humanity Manitoba has built homes for more than 275 Manitoba families since 1987, with the help of thousands of volunteers and partnerships with local businesses and faith groups.
Volunteers and construction workers are currently building 14 affordable homes for low-income families.
"We're trying to help people who are economically challenged. They are having a tough time making ends meet as it is," Hopkins said.
"We like to have every dollar that we raise go directly into our program and get the houses built."
Hopkins said a neighbourhood watch program has been set up, with nearby residents urged to call 911 if they see anything suspicious at Habitat construction sites after workers and volunteers go home for the day.