Nine months after the formation of the NAP Government, it was overthrown by Zulfiqar Ali Bhutto, who used Akbar Bugti's allegation that Ataullah Mengal's regime wanted to disintegrate Pakistan and liberate Balochistan as grounds for this dismissal.

In 2002, the party didn't compete in the elections in protest of General Pervez Musharraf's October 1999 military coup which allowed the pro-military religious alliance to win almost all the moderate and nationalist constituencies.

BNP had vehemently criticized the government when the operation in Balochistan had been launched[6] and after Bugti's death all four of its independently elected representatives resigned from their seats of the National and Provincial Assemblies.

[7] In December 2006, Akhtar Mengal was arrested for allegedly ordering his security guards to beat up secret service personnel.

Mengal maintained that these secret service officials had tried to kidnap his children as they returned from school and as a result, the security guards had beaten them.