In a brash response to the government's claim he was dead, Pakistan Taliban chief Hakimullah Mehsud appeared in a video broadcast Monday.
Hakimullah Mehsud and Waliur Rehman will share control, but analysts say infighting could erupt again.
The arrests show that militants still pose a threat throughout the country despite the death of Taliban leader Baitullah Mehsud.
A council picked Hakimullah Mehsud to head the alliance, two days after another senior figure said he had taken over. The announcements may signal infighting, which in recent weeks has led to bloody clashes.
Meanwhile, another US airstrike on South Waziristan – like the one that targeted Baitullah Mehsud – killed 10 suspected militants Tuesday.
A reported shootout over who will succeed Baitullah Mehsud as chief may have killed one top candidate and critically injured another.
Without the charismatic Baitullah Mehsud, feuding Islamist militants could splinter.
As the government prepares for a major operation in South Waziristan, it's eyeing lessons learned from previous campaigns that were cut short in the face of weak public support.