The email emerged only on Tuesday night, on the eve of the latest hearing to update the High Court on the progress of damages claims by up to 100 victims of hacking.
Neither the name of the executive who sent the email nor its exact content were divulged at the hearing, but it is likely to form a key part of the evidence against NI in the civil claims and could also be used in any criminal trials that follow.
David Sherborne, representing some of the hacking victims, said the email contained an instruction relating to the telephone of a "well-known individual" and was of "enormous significance".
He said: "We don't know where this document was found, on whose computer, which inbox, which outbox."
Mr Justice Vos, the judge who will try the cases, said: "It was sent by an executive whose identity you know."
No further details were given in court, although Hugh Tomlinson QC, who is also representing hacking victims, said the email was "absolutely crucial and important".
Up to 100 new claimants, including Sir John Major's former daughter-in-law Emma Noble, are due to have their claims against NI heard next February in a second wave of claims, following the settlement of more than 50 claims earlier this year.
Mr Sherborne said the email, which emerged in March during manual searches of NI's records by the law firm Linklaters, which was acting for News International in the context of other proceedings, should have been disclosed earlier.
The legal firm did not alert lawyers conducting the civil litigation - for which it has apologised - and the claimants were only told about it by the police, he added.
The court has previously been told that police have discovered 4,791 potential hacking victims, of which 1,892 had been contacted by the police. Scotland Yard has said there are 1,174 "likely victims", suggesting NI may face hundreds more claims before it can move on from the hacking scandal.