The seizures are the latest in a long list of items confiscated by police as Madrid pulls out the stops to prevent the northeastern region from staging the vote on Sunday.
"The Guardia Civil (police force) seized 2.5 million ballots, four million envelopes and 100 ballot boxes in a warehouse in Igualada," said the source, speaking on conditoin of anonymity.
These are the first ballot boxes to be seized by police in the crackdown on the referendum.
The source said the company involved alleged the ballot boxes were "for elections at FC Barcelona," without giving further details.
A spokesman for the football club confirmed that the company had indeed provided FC Barcelona with ballot boxes for elections of its president in the past, but could not comment further.
Catalonia is deeply divided over independence, but an overwhelming majority of people want to vote to settle the matter once and for all, polls show.
The Constitutional Court, though, has ruled the referendum illegal, which is why Madrid is trying to stop it at all costs, using the legal means at its disposal.