The chief's family said they did not permit the Friday burial and had not seen proof of the leader's death.
Bugti, 79, was killed when the cave he was in collapsed during fighting with government forces who had earlier attacked his hideout in the hills of Pakistan's poorest and least populated province.
The killing generated widespread protests and the funeral has enraged relatives and ethnic-Baluch tribespeople.
Aljazeera said political leaders in Baluchistan are preparing to organise more demonstrations.
Bugti's son, Jamil, accused the government of defying family wishes to bury Bugti in Quetta, the provincial capital, and quietly burying him in a place where it was unlikely to set off anti-government protests.
Jamil said: "They have killed my father, now they are deciding where to bury him, without his family's permission.
"The government is scared the people will show their anger if my father is allowed to be buried in Quetta."
Abdul Samad Lasi, the area's top government official, said a plywood box containing Bugti's body and sealed by two locks was buried in a graveyard in the Baluchistan town of Dera Bugti.
Only 20 people attended the burial, including government officials and Dera Bugti community leaders.
Security forces surrounded the grave as barefooted workers wearing turbans set the coffin into the red earth and covered it with stone slabs.
A file photo of Bugti somehwere
in Baluchistan in May this year
Journalists at the graveyard, said to contain other members of Bugti's family, demanded the coffin be opened so they could see the body.
But Lasi said it was "illegal to show Bugti's face" and that he and a local Islamic cleric had earlier viewed the body and confirmed it to be the chief's.
Lasi said: "The body was badly decomposed. It was not in a condition to have been shown."
The burial comes amid heightened tensions in southwestern Baluchistan province, where widespread violence and anti-government protests have left at least six dead, dozens wounded and hundreds arrested.
Many of Bugti's relatives, including his children, live in Quetta, Baluchistan's largest city with a population of about 300,000.
Bugti's killing sparked off days
of protest in Pakistani cities
A funeral prayer service held for Bugti in the city earlier this week was attended by at least 10,000 mourners and followed by violent protests and clashes with security forces.
The Pakistani army announced that soldiers retrieved Bugti's body late on Thursday.
Bugti, a former Baluch governor turned militia leader, fled to the cave in Kohlu, southeast of Quetta, after President General Pervez Musharraf survived a rocket attack in the area in December.
Officials blamed ethnic-Baluch tribesmen for the attack, but Bugti never claimed responsibility.
The government says its security forces did not intend to kill Bugti in the weekend operation 265km east of Quetta, which left more than 20 people dead.
Opposition parties have demanded an inquiry into his death, and the length of time it took to recover his body has added to speculation over the official account of his death.