Prime Minister Khan arrived in Tehran late on Sunday after first visiting the shrine of Imam Reza (AS) in the northeastern city of Mashhad.
The incident came after a February attack in eastern Iran that killed at least 27 Iranian security personnel that Iranian authorities said was carried out by the Pakistan-based Jaish al-Adl group.
"We agreed to increase the security co-operation of the two countries, our border forces, our intelligence forces", Rouhani said during the conference, which was broadcast live on state TV.
"It is in the interest of both of our countries that there is peace in Afghanistan", Khan said. We will not allow any militant group to operate from our soil.
He said though terrorists are making efforts to cause harm to friendly relations between the two countries, Pakistan is determined to fight them.
Balochistan, which borders Afghanistan and Iran, is Pakistan's largest and poorest province, rife with ethnic, sectarian and separatist insurgencies. An alliance of those group, the Baloch Raaji Aajoi Sangar (BRAS), claimed responsibility for last week's bus attack.
Quoting Qureshi, The Express Tribune further reported that six steps have already been taken to make the Iran-Pakistan border more peaceful.
Pakistani officials said the group's base of support extends into the Iranian border territory where the militants have "training and logistic camps".
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Iranian foreign minister Javad Zarif condemned the attack, saying enemies of Pakistan-Iran ties were responsible for it.
"Full appreciation must be made for our security agencies, with the way they tackled terrorism in Pakistan", the premier said. "This is not in any way helpful for anyone".
President Hassan Rouhani said on Monday that Iran and Pakistan are determined to expand relations and no third country can undermine their friendly ties.
"It is a vast area and the control over the area is hard, it makes it easy for groups to be active on both sides", he said. It has also been decided that aerial surveillance of the Pak-Iran border will be done through helicopters, he added.
The ambassador said that Karachi needs a circular railway and China is ready to help Pakistan."We need more time to finalise a proper financial package", he added.
Rouhani also said the two sides discussed the regional situation, where Iran has been locked in direct and indirect confrontations with regional rival Saudi Arabia for years.
The prime minister said if the Kashmir issue is settled the entire Indian subcontinent will benefit from it and in that case Iran can reach the Indian and Chinese markets through the Pakistani soil. He thanked Rouhani for the hospitality and respect extended to the Pakistani delegation.
"Whether it can be achieved or not, that is to be seen".