Earlier, Pakistani officials said they had "credible evidence" that Baitullah Mehsud had been killed.
But senior Taliban commander Hakimullah Mehsud then contacted the BBC to say his chief was alive and well.
Officials in Islamabad later said that Hakimullah was himself one of those killed in a fight over succession in South Waziristan.
The BBC's Aleem Maqbool, in Islamabad, says the situation is very unclear and information is based on rumours from deep inside militant territory in north-west Pakistan.
In Washington, US National Security Adviser Jim Jones put he level of US certainty that Baitullah Mehsud had been killed "in the 90% category".
The Pakistani interior minister have challenged the Taliban to prove its leaders are still alive.
But Taliban commanders have dismissed this as a ploy to flush them out into the open.