Pakistan has banned the Saeed-led JuD and FIF from collecting donations on Monday, after President Donald Trump accused Islamabad of giving nothing to the US but "lies and deceit" and providing a "safe haven" to terrorists.
The government has banned companies and individuals from making donations to the JuD, the FIF and other organisations on the United Nation Security Council sanctions list.
The Securities and Exchange Commission of Pakistan (SECP) issued a notification prohibiting the collection of donations by the JuD, the front organisation of banned outfit Lashkar-e-Taiba, as well as several other such organisations named in a list of banned outfits by the UN Security Council.
"We have taken action against the JuD and the FIF not on the pressure of the Trump administration. We have initiated action against Saeed's organisations after 'serious deliberations'. It is not taken in haste," Mr Khan told BBC Urdu.
He said the action was part of the 'Operation Radul Fasaad', launched in February last year by the Pakistan military to disarm and eliminate the hidden terrorist sleeper cells across the country with support of local law enforcement agencies.
"We have taken action against the organisations which are on the UNSC sanctions list, so that our children remain safe in schools. We do not want that one day they (people associated with these organisations) attack their own country with guns," the minister said.
The PML-N government is also considering taking over the control of charities run by the JuD and the FIF. If action is taken, the JuD may lose its headquarters in Muridke, near Lahore, to the government.
The FIF is a Pakistan-based organisation that is closely connected to banned terrorist group LeT and JuD. It is also said that FIF is JuD with a new name, designed to evade scrutiny and sanctions.
Yesterday, JuD and FIF activists held a rally outside its headquarters in Muridke near Lahore in protest against the government action and also blocked a road.
Addressing the rally, JuD leader Hafiz Abdur Rehman Maki alleged that the action against the JuD and the FIF has been taken on the pressure of the US and India.
"Those trying to strangle the JuD and the FIF will soon be in the grip of Allah. We are not committing any crime to serve the humanity," he said.
Mr Maki also said that any move by the government to take the control of 'Markaz-e-Taiba' (the JuD headquarters) and charity would not be accepted.