The pro-independence group contacted BT after it received a media inquiry last week that appeared to contain information from internal correspondence, according to reports.
Police Scotland said the matter was under investigation.
A Yes Scotland spokesman said: “We can confirm that a complaint has been made to Police Scotland regarding unauthorised access to Yes Scotland e-mail.”
Yes Scotland has not revealed the content of the e-mails, which came from a personal account linked to the campaign, and said it did not know who accessed them. The group contacted police after BT looked at the account and produced a printout that appeared to show it was accessed “a number of times”.
First Minister Alex Salmond addressed the allegations on STV News. “It’s a very serious matter indeed,” he said. “There is a limit to what we can say because obviously it is now a police inquiry.
“But what I would say is that if it turns out that a newspaper has been involved in some way, given everything that has happened over the last few years with illegal hacking and the whole scandal that erupted from that, if that turns out to be the case then it would be a very serious matter indeed.”
The development follows a series of setbacks for Yes Scotland. It emerged last month that both Jacqueline Caldwell, the director of operations, and Susan Stewart, the director of communications, were quitting their posts in the organisation.