Pakistan risks losing at least £100 million worth of aid by kicking out a group of UK charities and international development organisations, it has been claimed.

Eighteen foreign non-governmental organisations (NGOs) were told earlier this month that they had 60 days to wind up operations after being denied official registration.

The organisations, including UK-based charities Plan International and International Alert, were given no official reason for the interior ministry ban.

However it is thought Imran Khan's government made the decision under pressure from Pakistan's powerful military spy agency which has accused foreign aid organisations of being a front for espionage.

Previous expulsion notices have accused organisations of “pursuing an anti-state agenda”.

Diplomats are understood to be trying to persuade Islamabad to reverse the ban, with the British government describing the evicted organisations as “important partners for the UK”. The aid groups deny wrongdoing and say their programmes are carrying out vital work that helps Pakistan's government and people.

An assessment of the ban's impact drawn up by aid groups and seen by the Telegraph estimates the expulsion will deprive Pakistan of at least £100m of aid programmes and halt projects helping up to 11 million people. Between them, the expelled organisations also directly employ more than 1,100 staff in Pakistan.

The aid organisations are trying to win a reprieve, but have only been told they can reapply in six months. A source familiar with the negotiations said there appeared to be no pattern to the evictions. Both religious and secular organisations have been targeted, from several different countries. The aid groups are carrying out work ranging from emergency relief to tackling mental health, child labour, governance and agriculture.

Much of Plan International's work has focused on better education, particularly for girls, and helping young people improve their livelihoods. The charity has also worked on sanitation and providing emergency relief.

“We are deeply saddened by the government decision and extremely concerned about the impact it will have on communities, particularly hundreds of thousands of children the organisation is currently supporting, as well as our own staff – who are all Pakistani nationals,” said a spokeswoman for Plan International. The charity said it had helped 1.6 million children since starting work in Pakistan in 1997.

A spokeswoman for World Vision said: “Whatever the reason, we believe that the price will be paid by the children of Pakistan whom we will no longer be able to reach with life-saving help.”

Pakistan has hardened its stance on foreign aid and advocacy organisations and in 2015 asked them to re-register so they could better be monitored.

The expulsions comes as human rights activists have raised increasing concern about freedom of expression in Pakistan.

ActionAid, a Johannesburg-based charity among the 18, has called the expulsions “a worrying escalation of recent attacks on civil society, academics and journalists”.

Shireen Mazari, minister for human rights, has called those allegations absurd and arrogant and likened the strict registration process to strict visa controls for Pakistanis heading to Europe. Officials have pointed out that dozens of other NGOs had successfully been granted registration.

The unsuccessful NGOs were first told they must leave in December 2017, but then allowed to appeal after international pressure. None of the appeals seemed to have succeeded.

An intelligence official told Dawn, a leading daily paper, that some of the NGOs were contributing to a “hybrid war” against Pakistan and also “encouraging sectarianism, promoting a foreign agenda, supporting hostile spy agencies, collecting illegal data and operating without any legal backing.”

A spokesman for the British High Commission in Islamabad said: “These organisations are at the forefront of vital humanitarian and development work and are important partners for the UK. We are urgently working with the Pakistani government to resolve these issues.”

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