The court in Balochistan's provincial capital Quetta acquitted former president Musharraf, ex-provincial home minister Mir Shoaib Nosherwani and Qaumi Watan Party chief and member of National Assembly Aftab Ahmad Khan Sherpao.
After the announcement of the decision by Judge Jan Muhammad Gohar, the lawyer representing Bugti's son Jamil Bugti, Sohail Rajput, announced his decision to challenge the judgment of the court, the Dawn reported.
"They should have been convicted and I do not understand why the court set them free," Rajput said.
"We are not satisfied with this judgement and we will challenge it," Rajput told reporters outside court.
Musharraf, 72, was indicted in the case in January 2015.
The court also rejected the request by Jamil to order exhumation of the body of his father to confirm that the body buried in Dera Bugti was that of Akbar Bugti.
In a separate application, Jamil had requested the court to summon the members of a parliamentary committee who had met Akbar Bugti following the violence in Dera Bugti in March 2005 in which dozens were killed.
Jamil had named Musharraf, former Prime Minister Shaukat Aziz, former Governor of Balochistan Owais Ahmed Ghani, ex-interior minister Sherpao and others for the murder.
Bugti, former chief minister of Balochistan and head of his tribe, was killed in 2006 in a military operation ordered by Musharraf who was president and army chief at the time.
His killing sparked nationwide protests and further fuelled an armed insurgency that began in 2004 in Balochistan.
Two co-accused -- Musharraf's then interior minister Sherpao and ex-provincial home minister Nusherwan -- were also indicted for their alleged role in the murder of Bugti.
Musharraf never appeared in the court during the entire legal process which had been in progress since 2009. He was also absent when the charge-sheet was read out in the court.
Musharraf came to power in a bloodless coup in 1999, deposing then-prime minister Nawaz Sharif. Facing impeachment following elections in 2008, Musharraf resigned as president and went into self-imposed exile in Dubai.
The ex-army chief is facing a slew of court cases after returning from five years of self-exile in Dubai to contest the general elections in 2013 which he lost.
He is also facing trial in high treason case for abrogating the constitution in 2007 and illegal detention of judges same year.
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