The News of the World reacted to the unexpected arrest of one of its most senior reporters by clearing his desk.

Despite the paper having promised that it would co-operate fully with police inquiries, executives descended on the desk of former news editor James Weatherup moments after learning of his arrest. Under the eyes of their legal team, they bagged up notebooks, papers and recording machines and removed them "via our lawyers", a firm whose identity the publisher refused to confirm.

A few hours later, the police arrived and took the bags to Scotland Yard.

The unexpected arrest of Weatherup, one of the most senior journalists at the News of the World, at his home leaves little room for doubt that the new police team investigating the phone-hacking scandal is determined to succeed where its much-criticised predecessors failed.

It was three weeks ago that the News of the World dumped a vast archive of data at Scotland Yard's door – a trove that has turbo-charged the Met investigation.

The data, which comprises millions of emails from everyone at the newspaper – and which the NoW previously claimed had been lost – could implicate the paper in more instances of malpractice than have been previously suggested.

There are 8,000 emails relating to Sienna Miller alone. An examination of their contents could reveal that many more public figures were targeted by the newspaper, in addition to the 24 who are already bringing legal actions, including football agent Sky Andrew and the former culture secretary Tessa Jowell.

It was also anticipated that the archived data would include email exchanges between the most senior executives on the NoW, including its former editor Andy Coulson, who resigned as David Cameron's media adviser in January, and Ian Edmondson, Greg Miskiw, and Neville Thurlbeck, journalists on the paper. Edmondson and Miskiw had already been implicated in the affair by paperwork seized from Glenn Mulcaire, the private investigator who was on the NoW's books.

What was not expected, however – even by the most senior executives at the paper – was that a new name would be discovered amid the mountains of data, along with evidence so strong that an arrest could be made.

Weatherup's arrest stunned those at the highest level of the paper. News International executives have been saying privately that they were confident Edmondson and Thurlbeck were the only staffers still working at the paper who were likely to be implicated in hacking. The Met was so determined to conceal the new direction of its investigation that Weatherup, 55, was not given notice that he was being investigated by police officers.

Unlike his colleague and former colleague Thurlbeck and Edmondson – who were arrested last week on suspicion of unlawfully intercepting mobile phone voicemail messages – he was not given the chance to voluntarily attend a police station before being placed under arrest.

Instead, Weatherup – the third news editor under Coulson and one of a handful of senior employees who would take part in private discussions of major news stories with other senior members of the paper – was arrested in an early-morning swoop that left both his family and News International reeling.

Not only was his house in Romford, Essex, searched but also the contents of his desk are now being examined by police – the third time Scotland Yard has seized all official and personal material belonging to a NoW employee in little more than a week. What is also significant about yesterday's arrest of a hitherto relatively unknown figure is that the police have worked at such intensity and speed.

Until last week, former royal editor Clive Goodman, jailed in January 2007, was the only News of the World journalist to be arrested for listening to private voicemail messages. No other reporters or executives were questioned in the initial police investigation. It was only after a series of high court cases brought by Miller, the football pundit Andy Gray and others that the Met was forced to reveal material found on Mulcaire's computer, during a 2006 raid of his home.

In contrast, the 45-member new team, Operation Weeting, have arrested three current or former NoW journalists in the past nine days alone over possible involvement in alleged phone hacking at the paper.

• This article was amended on15 April 2011. Originally the article stated that "detectives also conducted a search in the tabloid newsroom while staff were asked to decamp to a nearby bar." This was incorrect and has been deleted.