He said the party's outgoing general secretary, Tom Sawyer, had got legal backing for the move, adding that the row was about "an interpretation of what I think was a not very elegantly drafted rule.
"Tom's taken legal advice and he's very clear that what the party's done, as you'd expect, is entirely consistent with the law," the Home Secretary told BBC Breakfast with Frost.
Left-wingers cried "foul" after Mr Sawyer said party members who had not renewed their membership could still vote in the telephone ballot.
Mr Sawyer and the leadership are fighting to stop a string of left-wingers being elected to the executive at next week's party conference. They were described by Neil Kinnock, the former leader, last week as "Trotsykites, sectarians and other selfish parasites".
There are suspicions that many of the supporters who joined in the flush of the election landslide and have not renewed their membership are Blairites and will oppose the left-wing slate. This includes Liz Davies, who was blocked as a Labour candidate in Leeds North East by the NEC.
Mr Sawyer said: "I am satisfied that ballot papers for the NEC elections have been sent to Labour Party members who are eligible to vote and only to those eligible to vote.
"The franchise for the 1998 ballot is exactly the same as for all previous ballots for the NEC."
He said there was "some confusion" over the application of the new membership rules, adopted at last year's conference, arguing they were "only ever intended to apply to selections of parliamentary, European, Scotland Parliament and Welsh Assembly candidates".
Mr Sawyer further insisted that when the matter had been drawn to his attention, he took legal advice which "supported my decision to err on the side of caution in allowing the relevant individuals to vote".
The party would have been "open to legal challenge" because it had not notified people they had been disenfranchised, he added.
Liam Fox, the Tory Constitutional Affairs spokesman, accused the Labour leadership of "vote rigging".
"It merely confirms what has long been suspected about Tony Blair; that winning is everything and that scruples and integrity must never stand in the way of victory.
"The people of Britain should take this as a public warning about Labour's intentions to rig the electoral system for the whole country if Tony Blair believes that is in his best interest to do so."Reuse content