Pakistan officially objects to strikes on its territory by the pilotless US aircraft, although Tuesday's attacks came as the Pakistani army was preparing to launch an offensive against the leader of the Pakistani Taliban, Baitullah Mehsud.
Asked by Al Jazeera to comment on Tuesday's reported attacks, the Pentagon denied any US involvement.
"There are no US military strike operations being conducted in Pakistan," a statement said.
Al Jazeera's Kamal Hyder, reporting from Islamabad, said reports suggested that the leader of the Pakistani Taliban may have been attending the funeral ceremony when it was hit.
"There are reports that Mehsud himself was at that congregational prayer and escaped the attack.
"However, we are told that a number of people present at that particular moment were killed," he said.
"There were unconfirmed reports that the death toll is much higher because a number of the bodies are badly mutilated."
The missile strikes came on the same key rival of Mehsud, Qari Zainuddin, was assassinated the northwestern town of Dera, police said.
Zainuddin, a Taliban commander, had spoken out strongly against the Taliban chief and may have been about to mount a challenge against him.
Pakistan's military mounted an operation earlier this month against Mehsud in South Waziristan.
But our correspondent said Tuesday's attack is likely to cause considerable anger and backlash in the country.
"It may play into the hands of elements like Mehsud because the attack took place on a funeral - there are cultural sensitivities here as well," he said.
"Such attacks are likely to complicate the situation for the Pakistani military because they have to be equally sensitive to public opinion in that area - something that is not going to be helped by the drones."
Frequent attacks by pilotless US drone aircraft have been heavily criticised by Pakistani leaders for killing innocent bystanders and infringing upon national sovereignty.
The US considers Pakistan's tribal region, of which South Waziristan is a part, a hideout from where al-Qaeda and Taliban fighters launch attacks on US forces in Afghanistan.
Mehsud, an al-Qaeda ally, is accused of plotting the assassination of Pakistan's former prime minister Benazir Bhutto in 2007.
The US government has offered a reward of $5m for information leading to his location or arrest.