Each ETA permits multiple journeys to the UK for stays of up to six months at a time over two years, or until the holder’s passport expires if that is sooner.
Heathrow airport blamed the ETA scheme for a 90,000 drop in transfer passenger numbers on routes included in the system since it was launched.
It described the programme as “devastating for our hub competitiveness” and urged the Government to “review” the inclusion of airside transit passengers.
Ms Cooper also announced the introduction of a visa requirement for all visitors from Jordan from 3pm on Tuesday due to breaches of visitor rules.
Jordanian nationals will no longer be able to travel to the UK with an ETA.
A four-week “transition period” will be in place for travellers who already hold an ETA and have confirmed travel bookings.
Ms Cooper wrote: “We are taking this action due to an increase in the number of Jordanian nationals travelling to the UK for purposes other than what is permitted under visitor rules since the visa requirement was lifted in February 2024.
“This has included a significant and sustained increase in asylum claims, and high rates of refusals at the border due to people travelling without the intention of visiting for a permitted purpose.”
This has “added significantly to operational pressures at the border”, Ms Cooper wrote.
She added that the decision to introduce a visa requirement was taken “solely for migration and border security reasons”, and the UK’s relationship with Jordan “remains a strong and friendly one”.