Confusion over postal voting emerged after complaints from expats that they had not received their ballot papers in time.
Voters living abroad in three continents told a national newspaper that they were forced to miss the historic poll because of administrative errors and delays.
A record 46.5 million people were eligible to vote in the referendum including British citizens living overseas who have been registered for UK elections within the past 15 years.
The Electoral Commission said postal votes were dispatched by counting officers in batches and applicants were encouraged to register as early as possible.
A spokesperson said: 'Postal votes will have been issued throughout the referendum period, but anyone who applied very close the application deadline will not have been sent a postal vote until the final update to the register on 20 June.'
