"It [sheltering Rigi] is not in the interest of the two countries' good neighbourly relations."
A statement from the Pakistani interior ministry following the talks made no reference to the request for Islamabad to hand over Rigi, but instead denied any Pakistani backing for Jundollah.
"Pakistan would never allow its territory for any terrorist activity against Iran or any other country," an interior ministry statement quoted Malik as telling Najjar.
In the past, Islamabad has denied that Rigi is in Pakistan and has accused the Jundollah of trying to undermine its close ties with Tehran.
Iran has previously suggested that the fighters have links with Pakistani intelligence, and also accuses the United States and Britain of backing Jundollah.
Washington, London and Islamabad have all denied involvement.
Iran's remote Sistan-Baluchestan province has seen an increase in bombings and clashes between security forces, ethnic Baluch Sunni fighters and drug traffickers.
Many Baluchs in the Iranian province feel more closely aligned with Baluchs in Pakistan's neighbouring Balochistan than with Iran's majority, mainly Shia, Persian population.
Iranian state television said on Tuesday that three people had been detained in connection with the Pisheen bombing, but gave no details.
At least 15 Revolutionary Guards, including six senior commanders, and 27 other people were killed in the blast.