Duffy and a second man were detained by officers in Lurgan, County Armagh, just miles from where David Black was assassinated in a drive-by shooting.
After being shot, the 52-year-old's Audi A4 veered off the M1 and crashed into a deep ditch.
Duffy and the second man, 31, were taken for questioning by detectives at Antrim.
Duffy, 44, was acquitted by a judge in Belfast earlier this year of the murders of two soldiers shot dead by dissident Republicans outside Massereene military barracks in Antrim in March 2009.
Mr Black, from Cookstown, County Tyrone, was shot dead as he drove to begin duties at Maghaberry Prison, near Lisburn, County Antrim, yesterday.
Prime Minister David Cameron and all sides in Northern Ireland condemned the shooting.
In a statement to the Commons today, Northern Ireland Secretary Theresa Villiers said the Government would do "whatever we can" to help bring Mr Black's killers to justice.
It was also discussed today at a north south ministerial meeting in Armagh involving Enda Kenny, Taoiseach of the Irish Republic, Northern Ireland First Minister Peter Robinson and Deputy First Minister Martin McGuinness.
Duffy faced separate murder charges on two other occasions and was cleared both times, once by the Court Of Appeal.
Mr Black is the 30th prison officer killed in Northern Ireland since 1974, but the first for almost 20 years.