Chinwoke Mbadinuju, former governor of southeastern Anambra state, was charged with the 2002 murder of prominent lawyer Barnabas Igwe and his wife Abigail. Igwe was a critic of Mbadinuju's government.
The killing of the couple will join a long list of unresolved political murders in Africa's most populous country.
The charges against Mbadinuju were a rare attempt by prosecutors to hold a senior figure accountable for political violence, still a common problem in Nigeria nine years after it emerged from army rule.
Mbadinuju, who was governor from 1999 to 2003, had pleaded not guilty to ordering the murder of the couple when he was first charged in December 2005.
"On the face of the police investigation report ... the applicant has no case to answer for murder," High Court Judge D.O.C. Amaechina said in the ruling.
The Igwes were dragged from their car and shot as they returned from a party in Onitsha, the commercial capital of Anambra. The killers then hacked off the woman's leg and ran over the bodies with a car.
Igwe was chairman of the Onitsha branch of the Nigerian Bar Association, which immediately accused agents of the Anambra state government of the murders. Igwe had backed Anambra civil servants in a dispute with the governor over unpaid wages.
At the time, the Onitsha bar association threatened to boycott Anambra courts and called on then President Olusegun Obasanjo to declare a state of emergency in Anambra.
As governor, Mbadinuju enjoyed immunity from prosecution, but he lost his seat at a 2003 election.
The Onitsha murders came nine months after the unsolved assassination of Justice Minister Bola Ige, who was shot dead in his bedroom in the southwestern city of Ibadan.
Ige is the most high-profile name on a list of dozens of Nigerian politicians whose murderers have never been identified.
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