Peers rejected a Lib Dem attempt to block moves to accelerate the full switchover to individual registration.
From December, all household members must register by themselves or face being removed from the register.
Critics say “huge numbers” could be disenfranchised but ministers say “no genuine voters” will lose out.
To ease the transition to the new IER system, which was first agreed in 2013, nobody has so far been taken off existing electoral registers, but anyone who has not individually registered by 1 December will be removed.
Labour and the Lib Dems say by doing this then, rather than in December 2016 as was originally envisaged, risks robbing more than a million people of the chance to vote in next May’s elections, including polls for the Scottish Parliament, Welsh Assembly and new London mayor.
Opponents of the accelerated timetable for IER sought to block the measure through a so-called “fatal” motion but this was rejected by peers by 257 to 246 votes after a two-hour debate.
The Electoral Commission watchdog has called for the measure to be blocked by Parliament while work continues on the latest annual canvass of households to establish an accurate picture of current registered voters.
It says the risk of disenfranchising large numbers outweighs the chances of a smaller number remaining on the register who should not be.
Arguing for a delay, Liberal Democrat peer Lord Tyler, a former MP, said he had never heard a statutory body express its view with “such clarity”.
“The official estimate is that 1.9 million people who are currently on the register and were on it at the general election in May will be dropped off it,” he said. “At a stroke, ministers are prepared to disenfranchise huge numbers of electors.”
But speaking out against the motion, Conservative peer Lord Dobbs said opponents had not provided a single example of any individual who would lose out as a result of the move.
And government minister Lord Bridges said the purpose of the move was to “remove ghost entries”, people who had moved house, died or had never existed at all, a category of people he said accounted for 4% of those on the register at the general election.
He said such people had been given “ample opportunity” to confirm their identity, having been contacted by officials nine times.
No-one currently on the register “would lose their right to vote”, he told peers, insisting the government should not tolerate the risk of fraud and IER was a step to a “more modern and secure electoral system”.
Tuesday’s vote came at a time of growing tension between the Lords and the Commons over the authority of the appointed House to challenge government business following peers’ decision to demand major changes to the government’s tax credit cuts.