A “knee-jerk” decision by Theresa May to restrict the discretion of border staff to decide not to deport people sowed the seeds of the Windrush scandal, it has been claimed.

Lucy Moreton, general secretary of the ISU, the union for borders, immigration and customs staff, said on Friday morning it was “deeply unfair” for ministers to blame officials on the ground.

Seven years ago, May sacked the head of the Borders Agency, Brodie Clark, for using his authority to relax passport checks in order to reduce immigration queues.

“The discretion that these staff used to have in order to deal with individuals justly and fairly was removed in the wake of the scandal,” Moreton told BBC Radio 4′s Today programme.

“Previously we were able in immigration control and in immigration enforcement to take an educated, reasonable, experienced view,” she said.

“If someone told you that they had come to the UK on Windrush, or a similar vessel, that they had been here since the late 60s, or even just that they had been here pre the 1971 Act, you can talk to them a bit, you can understand if they’ve genuinely been here.”

Morton added: “It was a knee-jerk, a backlash reaction to what was perceived as an unfair exercise of discretion on the border control by Brodie Clark.”

May has been under intense pressure over reports thousands who answered the post-World War II call to come to the UK to work in essential services are wrongly being denied access to state healthcare, losing their jobs and even being threatened with deportation.

It was also revealed documents which had been used to establish when migrants arrived in the UK were destroyed by the Home Office in 2010 – when May was home secretary.

The prime minister has apologised to those who have been affected. But told MPs the decision to destroy the cards was made in 2009 – under the last Labour government.

Alan Johnson, who was home secretary at the time, told the BBC on Thursday evening it a was an “administrative decision taken by the UK Border Agency” of which he was not aware.

“It was an administrative decision, just at it was a year later, when Theresa May was home secretary – as my successor – and they were destroyed,” he said.

Jeremy Corbyn has accused May of being “callous and incompetent” in the wake of the scandal.

Labour has said current home secretary Amber Rudd should “consider her position”.

May is also facing fresh questions about the controversial “go home” vans deployed by the Home Office in 2013 to crack down on illegal immigration.

The prime minister’s former chief of staff Nick Timothy claimed May was opposed to the vans.

But according to Business Insider, a former home office official claimed May actually demanded the message on the vans be “toughened up”.