World Bulletin / News Desk
Ministers say they are considering urgent legislation to allow people applying after the deadline to vote and have promised updates when possible.
The Electoral Commission has called for legislation to extend the deadline.
The glitch, blamed on record demand, lasted from 22:15 BST on Tuesday until after the midnight cut-off.
Users reported a page displaying the message "504 Gateway Time-out" instead of the online registration form.
"Those registrations will be captured by the system - then we have the legal question about whether captured applications can be eligible for the 23 June," he added.
He said the aim was that everyone who wanted to was able to take part in "this great festival of democracy".
Opposition parties have expressed anger at the events and called for an extension to the deadline, with Lib Dem leader and pro-Remain campaigner Tim Farron saying it was a "shambles" that could affect the referendum result.
Conservative MP and Leave campaigner Bernard Jenkin said it might be legal to extend the deadline for a few hours, but said "any idea of rewriting the rules in a substantial way would be complete madness and make this country look like an absolute shambles" with a risk of a legal challenge to the referendum result.Last Mod: 08 Haziran 2016, 16:29