It is believed a window was broken and a explosive device hurled inside.
Minneapolis police said a preliminary investigation shows a destructive device caused the explosion, "in violation of federal law", and that the FBI has taken the lead in the investigation.
There were 15 to 20 people were gathered for morning prayers when the explosion occurred.
Mohamed Omar, the mosque's executive director, told reporters in Bloomington that a member of the congregation saw a pickup truck speeding away from the building's parking lot just after the blast.
After an initial response by Bloomington police, agents from the FBI and the federal Bureau of Alcohol, Tobacco, Firearms and Explosives joined the investigation.
Authorities in Bloomington said no one was injured in the blast at the city's Dar Al-Farooq Islamic Center.
The blast is said to have happened in the imam's office during the first prayer of the day, according to an official at the mosque in Minneapolis, Minnesota.
People make phone calls following an explosion at the Dar Al-Farooq Islamic Center in Bloomington, Minn.
A blast shook a rural Minneapolis mosque early Saturday morning, specialists said.
"If a bias motive is proven, this attack would represent another in a long list of hate incidents targeting Islamic institutions nationwide in recent months", said Amir Malik, CAIR's civil rights director in Minnesota. Paul metropolitan area, the Associated Press reported. "We are strong and we don't want to lose hope because of things that happen".
Asad Zaman, director of the local Muslim-American Society, condemned what he called "an arson attack" and said his organization will offer a $10,000 reward for any information leading to an arrest or conviction. The society urged "the community to be calm and remain safe". Worshippers managed to extinguish the blaze before firefighters arrived, according to a statement from the Muslim American Society of Minnesota. "It's a place where Minnesotans are gathering to create community, to talk to their neighbors, to learn about our world and each other, and to help care for children".