Allegations surfaced earlier this year that Ray Koop of Bethania Group Personal Care Homes had rigged a new contract to get around a provincial salary freeze.
Koop retired, started collecting a pension and was rehired the next day at a higher salary.
That contract was cancelled, but Manitoba Health Minister Theresa Oswald says there are new concerns about alleged financial mismanagement, staff intimidation and nepotism.
Oswald says the government raised the concerns with Bethania's board and it agreed that an independent investigation is needed.
Koop's questionable contract came to light after the province audited Bethania last December.
"These new allegations are numerous and serious and must be investigated," Oswald said in a release Friday.
"While inspections continue to show that the care at Bethania meets provincial standards, we also need to ensure that serious allegations about potential financial mismanagement and respectful workplace issues are investigated thoroughly."
Board chairman Jake Neufeld said Bethania takes the concerns seriously.
"In good faith, we will work with the reviewer and Manitoba Health to achieve a speedy resolution," he said.
During last year's audit, investigators learned that Koop had received a large pre-retirement payment on July 31, retired on Aug. 1, started collecting a pension and was rehired the next day with a salary increase. Before his retirement, he was earning $160,000 a year.
Bethania originally balked when the Health Department ordered the group to repay the money that exceeded Koop's previous contract.
Oswald said Friday the board has now agreed to return to the original contract and pay the money in dispute.