Mr Donaldson was shot dead by Real IRA gunmen in a rural cottage near Glenties in Co Donegal in 2006.
The former senior Sinn Féin official had confessed to spying for Special branch and MI5 months before he was killed.
The Donaldson family say they have questions about the alleged role played by police in the circumstances surrounding his death.
They recently met with Dr Michael Maguire to highlight their concerns after a previous investigation was closed.
In a statement on Wednesday, the Ombudsman confirmed he will take another look at the case.
"The Police Ombudsman's Office can confirm that it is looking at allegations about police conduct in connection with events surrounding the death of Mr Donaldson," a spokesman said.
"The Office had previously looked at these allegations. Since then, members of Mr Donaldson's family have brought new information to the Office which they were not previously aware of.
"The Police Ombudsman, Dr Michael Maguire, has decided that their allegations must be looked at again in light of this new information."
The family has welcomed the decision.
A statement issued through their legal representatives, Madden and Finucane, said: "After reviewing the family's original complaint, existing case papers and new information which has been uncovered, Dr Maguire has now written to the Donaldson family confirming that the case will be the subject of a renewed investigation.
"Dr Maguire has also confirmed that an extant and incomplete investigation by his predecessor left many unanswered questions of complaint and concerns.
"Since then, members of the Donaldson family have met with the Police Ombudsman's investigation team and have agreed to co-operate fully with the new investigation.
"We remain deeply concerned about the role of some PSNI officers who have held senior intelligence and investigative roles who may hold detailed information about the circumstances surrounding Denis's murder.
"The acid test will be whether these serving and retired police officers, and others, fully co-operate with this investigation by the Police Ombudsman. We are determined to hold these individuals to account."