Little's stance comes a day after AFL chief executive Gillon McLachlan insisted that no such agreement had ever been negotiated by the parties.
Little was an Essendon board member when the alleged agreement was brokered. He became club chairman in July 2013 after David Evans stepped down due to ill health.
After a long-running investigation that began in February 2013, ASADA issued show-cause notices to 34 past and present Essendon players this month.
"As a board member, we were of the view there had been an agreement reached and we were very surprised when ASADA had appeared to have gone back on what was the original agreement," Little said on Channel Seven on Saturday night.
It had been reported more than 50 emails between the AFL and ASADA were sent between February and March last year as the saga gathered steam.
McLachlan denied on Friday that the email chain contained any mention of a special agreement.
"We worked through with ASADA a framework that was put to the players about how the investigation was going to run, how the interviews were going to run and what sanctions were available under the code," McLachlan told radio station 3AW on Friday.
"That's what that referred to - the agreement that was read to the players about how the process was going to run and how the code worked and what was available."
Little said he was becoming increasingly frustrated by the length of the ASADA investigation.
"We were given certain timeframes on how long the investigation would continue. Clearly we're now well beyond that," he said.
