Uber secretly tagged its users' phones even after they deleted its app, according to a new report.

The invasive tracking led Apple to call the company for a special meeting where boss Tim Cook threatened to kick it out of the App Store and so off people's iPhones, according to the New York Times.

The tracking referred specifically to a tool that allowed Uber to watch for when people deleted the app and then find them again when it was re-installed. Uber claims that the tool was necessary to fight against fraud and that it is a common practice – but it was in contravention of Apple's privacy laws and was kept completely secret from the users being tracked.

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The trick relied on a special tool called "fingerprinting" that allowed Uber to identify the phones that downloaded its app. When someone then deleted it again, it kept that "fingerprint" and watched for it downloading the Uber app over again – allowing the company to know if it had been re-installed on the same phone.

The company said that it needed to do that so that it could ensure if a phone had been flagged for fraudulent activity, a user couldn't simply delete the app and start over again.

When Apple engineers found that secret trick, Mr Cook called Uber CEO Travis Kalanick in for a meeting, according to the New York Times report. He said “I’ve heard you’ve been breaking some of our rules,” according to the report, and threatened to remove the app from the App Store – a move that would likely kill of the multi-billion dollar app in one quick move.

Uber said that after the telling off it changed the fingerprinting so that it complies with Apple's rules. That means that it likely continues to track those phones.

“We absolutely do not track individual users or their location if they’ve deleted the app," an Uber spokesperson said. "As the New York Times story notes towards the very end, this is a typical way to prevent fraudsters from loading Uber onto a stolen phone, putting in a stolen credit card, taking an expensive ride and then wiping the phone—over and over again.

"Similar techniques are also used for detecting and blocking suspicious logins to protect our users' accounts. Being able to recognise known bad actors when they try to get back onto our network is an important security measure for both Uber and our users.”

Since the controversial tracking tool, Uber has actually added a feature to its app that does in fact allow it to track people when they've closed the app down. Last year, it added the feature and stressed that it will only track people for five minutes after their journey – a move that it said was being done to keep its users safe.

The same New York Times report also claimed that Uber was buying receipts from customers who were using Lyft, a rival taxi app. It then studied those receipts – bought from normal users – to understand how to better take on its rival, the report claimed.