Reports on Saturday said that both Hakimullah Meshud and Wali ur Rehman, two possible successors to Baitullah Mehsud, had been killed in the shooting.
But on Sunday, Wali ur Rehman purportedly told the Reuters news agency by telephone that there had been no shootout and they were both alive.
"There are no differences. There was no fighting. We both are alive, and there was no special shura meeting," he was reported as saying.
Hakimullah Mehsud served as a deputy to Baitullah Mehsud and Wali ur Rehman was a senior commander in the umbrella Tehreek-e-Taliban Pakistan (TTP) movement.
Rehman Malik, Pakistan's interior minister, said intelligence reports suggested that one of the two men had been killed.
"We have information that one of them has been killed. Who was killed we will be able to say later after confirming," he said.
"The infighting was between Wali ur Rehman and Hakimullah Meshud."
However, a Taliban official in South Waziristan insisted that the government had fabricated reports of fighting between the different factions.
Noor Said, a spokesman for the Pakistani Taliban, said: "There was no fighting in the shura. Both Wali ur Rehman and Hakimullah are safe and sound."
The reports have added to earlier confusion surrounding the reported death of Baitullah Mehsud, the Pakistani Taliban leader who had a US bounty of $5m on his head.
While the US administration has not confirmed reports of Baitullah Meshud's death, the White House appears to increasingly back the stories of his killing.
Asked on US television network NBC's "Meet the Press" programme if Baitullah Meshud had been killed, Jim Jones, the US national security adviser, said: "We think so. We put it in the 90 per cent category."
'Dissent and discord'
Syer Tariq Pirzada, a strategic affairs analyst in Islamabad, told Al Jazeera that the reported shootout strongly indicated that Baitullah Mehsud was "dead or functionally dead".
"Had he been alive, he was such a strong leader, he would not have allowed this dissent, this discord and this violent confrontation ... to happen," he said.
Earlier on Saturday, Hakimullah Mehsud had told reporters by telephone that Baitullah Mehsud was in good health and would soon appear in the media to prove that he was alive.
Mahmood Shah, a former security chief for the tribal regions, said that Hakimullah Mehsud's claims could have been part of the power struggle within the movement.
"I think that this denial from them ... doesn't appear to be holding much water," he said. "It should have come earlier and ... much stronger."
"There is, I think, a struggle going on for the leadership, and Hakimullah Mehsud is one of the contenders."