News International has ordered the mass deletion of hundreds of thousands of emails from its computer system in the past 18 months, MPs learnt last night.

The news has prompted concerns that vital evidence may have been lost to police and other authorities investigating the phone-hacking scandal. The extent of the deletions was revealed in a letter sent to the Commons Home Affairs Committee by lawyers acting for a technology company, HCL, which manages data for News International (NI).

A shocked Keith Vaz, chairman of the committee, said: "I'm very surprised that so many emails and information appears to have been deleted since the start of this year. This will raise further questions which I'm sure we will want to probe further but it's surprising that such a large number of messages have been deleted. Several thousand emails is a lot of emails." He said staff from HCL may be called to give further evidence before the committee.

Stuart Benson, a Reading-based law firm acting for HCL, detailed nine instances since April 2010 when NI had requested the deletion of emails. The first three requests were made within weeks of a Commons committee having castigated the company's executives for their "collective amnesia" over the extent of hacking by the News of the World.

In one of the requests, NI asked for the deletion of more than 200,000 pieces of correspondence. Another request, made the following month, asked for the deletion of 21,000 messages said to be "stuck in the outbox".

All of the requests for deletions could be due to standard practice in managing an IT system though other similar businesses said last night that they retained email archives for much longer. Two of the requests made references to "public folders" and investigators will want to be sure that these are not ruses used to disguise the identity of the user.

Scotland Yard detectives, who are examining the NI information systems for evidence of phone-hacking and illicit payments to police, are likely to be angry at any attempt to interfere with the archive, particularly since January this year when NI stated publicly that it was doing everything in its power to co-operate with the inquiries. Three of the requests for email deletions were made in 2011.

MPs who have led the campaign for a full investigation into hacking expressed their concern last night. Tom Watson, the Labour MP for West Bromwich East, said: "Sadly this is not a surprise but it's a shocking revelation and casts further doubt on the leadership of the previous investigation by the Metropolitan Police. I sincerely hope this means the police will now consider News International an unco-operative partner in trying to crack the cover-up of hacking."

Chris Bryant, Labour MP for Rhondda, said: "Some of us called from the very beginning for the Met to go in and seize the whole of the IT system. From what we have heard it seems we may never get to the bottom of how News International ..., in the words of the police, 'deliberately thwarted the investigation'."

In his letter to the committee, HCL's solicitor, Stuart Benson, said: "It is of course a matter entirely for News International, the police and your committee as to whether there was any other agenda or subtext when issues of deletion arose and that is a matter on which my client cannot comment and something which you will no doubt explore direct with News International."

Last night, News International made no comment on the letter.

News of the deletions follows a report in The New York Times that Harbottle & Lewis, a London law firm working for NI, had redrafted more than once a letter it sent to the Commons Culture Committee in May 2007, in effect clearing the company over further involvement in hacking. The Harbottle & Lewis letter said "no reasonable evidence" had been found that senior editors knew about the reporter's "illegal actions".

Next Monday victims of hacking by the News of the World who are bringing civil actions against the publishing company are due to be given disclosure of all the information held on them on the company's databases.

UPDATE: News International have put out a response to the letter sent on behalf of HCL to the Home Affairs Committee, today, which states:

“Since January, News International (NI) has been actively working with the police on Operation Weeting with regards to email data and other computer information which may be relevant to their inquiry.

“NI keeps backups of its core systems and, in close cooperation with the Operation Weeting team, has been working to restore these backups.”

On the trail of the deleted emails

February 2010

The Commons Culture Committee publishes a report accusing News International's executives of "collective amnesia" over the extent of phone hacking and says it is "inconceivable" senior executives did not know what was going on.

April 2010

First instance of email deletion occurs, with request to delete email boxes of certain people who have left the company. The request is not followed through as the emails are not impacting on the system. A second deletion request is made the same month and more than 200,000 delivery failure messages are deleted. A third request that month is for the deletion of a public folder by a specific user who "no longer needed older emails".

May 2010

A fourth request is made for the deletion of a further 21,000 emails which are said to be "stuck in the outbox". They are deleted.

July 2010

News International asks for another "public folder" to be deleted as part of "maintenance work" carried out on folders "no longer needed".

September 2010

The New York Times reports that hacking was widespread at the News of the World. It carries allegations from whistle-blower Sean Hoare, pictured top, who says such practices were "endemic". The Culture Select Committee orders a fresh inquiry. NI makes a sixth request for email deletions. HCL says this was for "pruning the historic email archives". NI argued that the deletions were needed to "help archival system which was having frequent outages".

January 2011

Scotland Yard asks NI for any new material they have regarding hacking. NI suspends the former News of the World news editor Ian Edmondson. Andy Coulson resigns from No 10. Met Police announce a fresh investigation. NI asks HCL about its ability to "truncate a particular database".

February 2011

Met Police say they have identified more potential victims of hacking. Judge orders private investigator Glenn Mulcaire, pictured left, to reveal whether other NOTW journalists knew about hacking. Eighth instance of deletion of NI emails as company asks to delete duplicate material from users who had switched systems.

July 2011