Justice Sean Harrington also issued an order on Friday morning to ban the reserve's executive council, band council and others from preventing Chief Alex James Robinson from carrying out his duties or from carrying out any band business voted at a meeting without the chief being present.
But whether Robinson will be able to begin acting as chief again is up in the air.
Robinson could not be reached for comment.
But Robinson's lawyer, Murray Trachtenberg, said "he (Robinson) was pleased by the decision.
"He has said he is the chief and he has tried to carry out his duties with no office, no cellphone, and no paycheque... all of that, the court says you have to stop that. The court has put him back as chief.
"We expect everybody to comply with the federal court order."
The injunction will be in place until the entire argument is heard in court. But by mid-afternoon on Friday, calls to the Cross Lake band office asking for the chief were still being directed to acting chief Garrison Settee.
When contacted, Settee said he didn't know all the details of the judge's decision.
"I will be talking to legal counsel -- that's all I'll say right now," Settee said.
Lawyer Robert Tapper, who acts for Settee and other members of the band's council, said Robinson can't begin acting as chief again because a separate matter before the courts -- contesting an order from the reserve's women's council removing him as chief -- still hasn't been heard.
"We're in a very grey area, but the women's council's edict is there and hasn't been dealt with," Tapper said.
Robinson has been battling to retain his position as chief almost since he was elected in August 2008.
His sister was charged in September with criminal negligence causing bodily harm and other charges after a 33-year-old female resident was struck by a van.
The RCMP charged Robinson and his brother in November with obstruction of justice after a witness accused the pair of trying to convince her to take the fall for their sister.
Those charges sparked the reserve's women's counsel to order the chief to leave office, saying he was "permanently incapacitated" because of the criminal charge against him. In Robinson's place, vice-chief Settee stepped in as acting chief until a byelection was to be held on April 2.
But in December, the reserve's elders council said they believed unseating the chief before the charge was heard was premature and they asked that Robinson be reinstated.
Earlier this month, the province's Justice Department announced it had dropped the charge against Robinson.
Cross Lake is located 520 kilometres north of Winnipeg.