The Ahmadzai tribe was fined 5.4 million rupees (US$95,000) under the law of "collective responsibility" for failing to stop the attacks.
The tribe was given two days to pay up or face "tough action," said Rahmat Allah Wazir, a senior government official in Wana, the main town in the deeply conservative South Waziristan region.
Pakistan's army has launched four military operations to track down al-Qaida suspects in the tribal region in the past two years.
In the latest, last week helicopter gunships and artillery raided three homes near Wana, arresting 25 suspects, although apparently none were senior al-Qaida figures.
The military has beefed up its presence in the fiercely autonomous region since the 11 September 2001 attacks on the United States, amid suspicions al-Qaida and Taliban holdouts - possibly including Usama bin Ladin - are hiding there.
Wazir said authorities had fined the Ahmadzai tribe for failing to prevent four attacks against the army in the past two months. It was not clear who carried out the attacks.
Under centuries-old tribal custom, an entire tribe is responsible for any crime committed by one of its members and can be punished collectively.
On Sunday, at least three rockets landed near an army facility in Wana, about 300km west of the capital, Islamabad.
Thirteen people were killed on
Saturday by Pakistani troops
"At their request, we have given them two days," Wazir said. "They will face ... tough action, if they do not pay."
Pakistan, a key ally in the US-led "war on terror", has used the tribal law in recent months to demolish the homes of several tribesmen for allegedly harbouring al-Qaida fugitives.
The army's actions have angered tribesmen - who share ethnic and cultural ties with Afghanistan's former Taliban regime.
Tensions have increased since Saturday, when Pakistani troops opened fire on a minibus after it failed to stop at a road checkpoint near Wana, killing 13 people. All the victims are believed to be civilians.
President Pervez Musharraf has announced compensation for the victims and an investigation into the shootings.
Wazir said he had told the tribesmen the government and the army was acting against "terrorists", and sought their support. "I am optimistic that they will cooperate," he said.