Ahmed Marouat spoke to Reuters news agency on Sunday, telling them that Merah had come to North Waziristan in the northwest of Pakistan to train with the Tehrik e Taliban Pakistan (TTP).
Afghanistan, Pakistan and their neighbours
However, they claimed that they had no information concerning Merah's attacks in France.
“That has no link to us,” said Marouat.
Two high commanders of the TTP also told Reuters that more than 80 French citizens were in North Waziristan and were part of the Islamist group Djihad e Islami.
The TTP was formed in 2007 and melds several army factions from tribal zones in Pakistan.
They describe their objectives as overturning Pakistan’s government, and initiating suicide attacks around the country.
A self-described Islamist, Merah told police he had committed his crimes to avenge the deaths of Palestinian children killed by Israel and to punish France for its participation in the Afghanistan conflict.
Merah shot and killed seven people in and around Toulouse between 11 and 19 March. Three Jewish children, a trainee rabbi and three soldiers were among the victims.
The week-long drama culminated in Merah's death by France's special police forces RAID, following a 32-hour siege of his home in Toulouse.