Police said they were questioning Abdullah Omar in the death of Federal Investigation Agency prosecutor Chaudhry Zulfiqar Ali in Islamabad May 3, Express News reported.
Zulfiqar was gunned down in his car by four men soon after leaving his home to attend a court hearing for a bail application by former President Pervez Musharraf.
The suspect was injured when the prosecutor's bodyguards fired back at the armed attackers who escaped in a car, the Express reported.
The BBC reported Omar is the son of a retired army colonel who was court-martialed 10 years ago for attempting to assassinate Musharraf.
Omar was captured later and hospitalized for a bullet wound to his spine he had received during the shootout with police, officials said. He was formally arrested while in a hospital.
The BBC said Zulfiqar has said in an interview he had received several death threats by telephone because of his investigations into the death of Bhutto and the 2008 terrorist attack in Mumbai, India, in which 166 people were killed.
He was believed close to submitting final evidence against seven members of the banned Lashkar-e-Toiba militant group who are on trial for helping plan the Mumbai attack, the BBC said.
Indian security forces killed nine of the 10 gunmen during the daring raid in central Mumbai. About 240 people were reported injured in the attack that lasted 60 hours.
The gunfight with police and the military severely damaged several well-known buildings, including the main train station Chhatrapati Shivaji Terminus, the Taj Mahal Palace and Tower Hotel, Hotel Oberoi-Trident, Cama Hospital and the Chabad House, a Jewish prayer center and the Leopold Cafe, a favorite among foreigners.
The surviving gunman, Mohammad Ajmal Amir Qasab, 24, was convicted in May 2010 of murder and waging war on India. He was given a death sentence and hung in November last year.
The arrest of Omar comes as Musharraf -- a former military ruler turned civilian politician -- was indicted last week for his alleged part in the detention of more than 60 judges during a nationwide state of emergency when he was president in 2007, officials said.
Musharraf, 69, denies all charges against him, KarachiNews.net reported Saturday.
Other charges against Musharraf, a former general, include counts stemming from the death of Bhutto in a gunfire and bomb attack while she was campaigning against him in 2007 and charges regarding the death of a tribal leader in 2006.
Musharraf's troubles began in March when he returned to Pakistan from self-imposed four-year exile in London and Dubai to run in last month's national parliamentary election as head of his All Pakistan Muslim League Party.
Arrests and detentions meant he failed to contest the election, which was won by Nawaz Sharif, 63 -- the man Musharraf toppled in a bloodless military coup in October 1999.
Sharif was installed as prime minister this month.
Musharraf is fighting charges in the August 2006 death of Baluchistan tribal leader Nawab Akbar Bugti, 79. Bugti, a former Baluchistan province minister turned nationalist rebel, was killed when a shell exploded in his mountain cave headquarters.
The Bugti case surrounds the circumstance in which the government raid on his cave took place and how the shell exploded.