Ten of the players are still at Essendon, while two are at rival clubs and another two are no longer in the AFL.
The Herald Sun claims that these players are at risk of being hit with infraction notices when ASADA conclude their investigation.
ASADA has finished stage one of the investigation, with the second review stage set to begin.
"Throughout this investigation, confidentiality has been paramount to protect the integrity of this process – unfortunately, at various times this process has been undermined by leaks, mistruths and a lack of ethical and professional behaviour," Little wrote in an open letter on the club's official website.
"Today the club is particularly disappointed that the Herald Sun would choose to provide confidential information from an incomplete and interim report that could easily and unfairly damage the reputation of our players.
"As previously stated, we believe that our players did not take anything harmful, performance enhancing or illegal during 2012.
"Our club is by no means in any crisis but we are particularly frustrated and disappointed that the Herald Sun has been unable to show the same level of professionalism and integrity as our players have done throughout this proces
"The disclosure of players names will not change the outcome of the investigation in any way whatsoever, however it unfairly impacts our players, their reputations, their families and our club.
"Our members and supporters should be proud of our players for the way they have conducted themselves through this process – they have cooperated fully, acted with professionalism, told the truth and not once compromised the integrity of this investigation."
The AFL Players' Association also took exception to the report in the Herald Sun.
"The AFL Players' Association condemns in the strongest possible terms the publishing of names and photos of current and former Essendon football players in today's Herald Sun," the statement read.
"The Players' Association calls on everyone to respect the process and integrity of the ASADA investigation – just as the players have done since this regrettable saga arose.
"For over 12 months, current and former Essendon football players have been the subject of an unprecedented investigation into failures of workplace governance and safety in Australian sport.
"For over 12 months, players have withstood enormous uncertainty, public scrutiny and speculation over their health, their careers, and their reputations.
"But for over 12 months, players have honestly, candidly and transparently cooperated with all authorities involved in multiple investigations.
"You would hope that by now, there might be some level of acknowledgment of the invidious position these young men have been placed in which is higher than publishing names and photos of some of them in a major daily newspaper in a manner which only fuels further speculation and uncertainty."
The AFL confirmed they are yet to receive any notification from ASADA about impending action against any player and added they will not comment until the investigation is completed.