Interior Minister Nisar Ali Khan told media that a high-level inter-ministerial committee recommended that NGOs should operate under the interior ministry.
"We are instituting a system to know where their money is coming from and how it is being used," he said.
He said the work is going on a comprehensive legislation to oversee the activities of aid groups in the country.
The minister also mellowed down his criticism of the NGOs and said at lot of them were doing work that governmental institutions could not do.
Khan also praised Save the Children which was banned this month for allegedly working against the interest of Pakistan.
"Save the Children is not an enemy of the state. It has been registered since 1997 and is a globally-recognised NGO," he said.
Save the Children was blamed for helping Dr Shakil Afridi to launch fake vaccination campaign in Abbottabad to verify the presence of Osama bin Laden who was killed by US Navy Seals in 2011.
Save the Children denied having any link with Afridi or the CIA.
