Yes Scotland's chief executive, Blair Jenkins, claimed the group's email accounts had come under attack from "a force or forces unknown" in what he called "an attack on democracy". Police are looking into the claims.
The IT shut-down prevented staff at the campaign's Glasgow HQ from sending emails or accessing the internet.
Mr Jenkins said: "The campaign for an independent Scotland is under attack from a force or forces unknown, clearly intent on causing as much disruption and damage to Yes Scotland and the movement as possible. Make no mistake, what this amounts to is an attack on democracy."
Yes Scotland called in police after a private email revealed details of a cash payment to an academic was accessed.
Yes Scotland has said the message related to a payment of £100 for an article by constitutional expert Dr Elliot Bulmer, research director of the Constitutional Commission charity, which was published by The Herald on July 13. The Herald was not made aware Dr Bulmer had been or might be paid by Yes Scotland.
Mr Jenkins said the payment was "entirely legitimate". He and Dr Bulmer have said Yes Scotland did not influence the content of the article, about a written constitution for an independent Scotland.
Scottish Labour has accused Yes Scotland of "deep dishonesty and deception".