Sources say it does not appear Brennan used the account for government business after he became CIA director.
"We are aware of the reports that have surfaced on social media and have referred the matter to the appropriate authorities," a CIA spokesman told ABC News.
Sources also say that an account linked to Homeland Security Secretary Jeh Johnson was also compromised.
"We are aware of the media report, however as a matter of policy, we do not comment on the Secretary's personal security." Sources familiar with the breach say it appears the Johnson hack exposed a very limited amount of information, none of it believed to be sensitive.
According to the New York Post, which first reported on the alleged intrusions after being contacted by an individual who identified himself as the hacker, the accounts were compromised through the use of "social engineering" techniques.
Social engineering typically involves leveraging open-source information about an individual to gain access to accounts by changing or resetting passwords.
The FBI and U.S. Secret Service are both investigating the alleged hacks. Sources say the matter has been ongoing and did not just pop on the radar of investigators last night.