"They had access at the required and appropriate level," Malik told Reuters.
"We are fully cooperating with Afghanistan and whatever they are asking for the peace process, for developing peace in Afghanistan. We are giving every kind of help."
Pakistan is seen as crucial to stability in Afghanistan as most foreign combat troops look to leave the country in 2014, given close political and economic ties and because militant sanctuaries straddle the mountainous border.
He was the right-hand man to reclusive Taliban leader Mullah Mohammed Omar, who gave him the nickname Baradar (brother), providing him with great influence and prestige in Taliban circles.
Afghan officials hope Baradar could play a key role in any negotiations to end the war, acting as a go-between with Taliban leaders including Omar.
Afghan and US officials have publicly acknowledged little success in efforts to re-start peace talks, which the Taliban suspended after accusing US officials of failing to honor confidence-building promises.
That setback refocused attention on nascent efforts by the Afghan government to open its own channels with insurgent intermediaries, despite the fact the Taliban publicly say they will not talk to what they deem an illegitimate "puppet" government.