The proscribed organisations will be examined under heightened security checks at all layers of legal, administrative, investigative and financial regimes, the Dawn newspaper reported.
The confiscation of properties of JuD and FIF comes after Pakistan formally placed them in the list of banned organisations on Tuesday.
The visit will be followed by the return visit of the Indian delegation to Islamabad on March 28.
India handed over a dossier to Pakistan to take action against the JeM, as pressure mounted on Islamabad to take action against individual and organisation listed by the UN Security Council as terrorists.
'Recording of his video message caused delay in his handing over'
The House rejected India's claims of having destroyed terrorist facility and causing heavy casualties as 'self-serving' and 'fictitious'.
Shah Mahmood Qureshi also claimed that Azhar is unwell to the extent that he cannot leave his house.
The report quoted Khan as saying that he 'tried to call Modi last night' (Wednesday).
Earlier, Pakistani military spokesperson Major General Asif Ghafoor claimed that two Indian Air Force pilots were arrested. One pilot is injured and has been shifted to a hospital, while another one is unhurt, the spokesman had said.
Khan said all wars have been started on miscalculations on the time and the human cost of war. This was the same with the World War I, with the World War II and the war on terror, the Pakistan PM added.
The country's top security body "concluded that India has committed uncalled for aggression to which Pakistan shall respond at the time and place of its choosing," it added.
Khan's remarks came a day after Modi in a rally in Rajasthan said, "There is consensus in the entire world against terrorism. We are moving ahead with strength to punish the perpetrators of terrorism..."
In his letter, Qureshi also accused the Indian government of using 'water as a weapon'.
Ghafoor warned that military response this time will be different in case of war.
A statement issued by the Interior Ministry also said the crackdown on Jaish 'has been taken in line with the decision of the NSC meeting'.
Secretary of Pakistan's ministry of water resources Khawaja Shumail said: "We have neither concern nor objection if India diverts water of eastern rivers and supplies it to its people or uses it for other purposes, as the IWT allows it to do so."
The JuD is believed to be the front organisation for the Lashkar-e-Tayiba.
Khan said the Pakistan government was 'determined to demonstrate' that it is capable of protecting its people.
Khan said, "If India has evidence or actionable intelligence, they should give it to us and we will take action."
India has rejected any third party intervention in the Kashmir issue and has maintained that all outstanding matters in Indo-Pak ties should be resolved bilaterally.
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