The watchdog said 4.1million Scots were on the electoral roll, with less than six months to go to the vote on September 18.
Yesterday the pro-independence and pro-UK campaigns both welcomed the record figure which, they said, pointed to a high turn-out on polling day.
The total is based on figures from Scotland's 15 regional Electoral Registration Officers (EROs) collated by the Electoral Commission.
It represents an increase of nearly 60,000 voters compared with December 2012.
However only 92,000 out of a possible 120,000 16- and 17-year-olds - who will be able to vote for the first time in the referendum - have so far added their names to electoral roll.
Andy O'Neill, head of the Electoral Commission's Scotland office, said: "The snapshot gives an indication of the hard work already put in by EROs, but that hard work doesn't stop now.
"EROs will continue to encourage as many people who are eligible to register to take action and get themselves registered before the September 2 deadline to take part at the referendum."
The Electoral Commission is planning a public awareness campaign in summer reminding people they must be registered if they want a referendum vote.
Blair Jenkins, chief executive of Yes Scotland, said: "The drive to encourage as many people as possible in Scotland to register to vote on September 18 is a key part of our independence campaign."
A spokesman for the pro-UK Better Together campaign said: "This is the biggest decision the people of Scotland will ever take so it's vital that as many people as possible have their say."
An increase in the number of students registering to vote has partly accounted for the rise, it is believed.
Kwaku Adjei, the president of Strathclyde University Students' Association said: "The referendum is an opportunity for all of us to say what kind of Scotland we want to live in."
The deadline for registering to vote is midnight on September 2.
Postal or proxy votes can be arranged up to 5pm on September 3 and emergency proxy votes, available under certain circumstances, can be arranged up to 5pm on polling day.