The Italian manager has taken the blame for his side's 3-1 loss in Amsterdam, after an ill-advised switched to three at the back prompted the hosts' third goal
The English champions took the lead against the run of play in the first half through Samir Nasri, but were pegged back on the stroke of half-time by Siem de Jong.
Mancini decided to switch to a 3-5-2 formation early in the second half following Niklas Moisander's headed goal, but City conceded again 11 minutes later through Christian Eriksen's deflected shot.
"I think that [Ajax] played better than us," Mancini told Sky Sports. "They played better football. Probably it's my fault. I didn't prepare the players well for this game. I take the fault for this defeat.
"I [prepared] one way, it was different. For this reason [we lost]. [We didn't underestimate Ajax], but when you prepare a game, you think it could be one way, but it's a different game.
"I think that we had more chances to score, and in Champions League you need to score, when you don't play well. After Dortmund, I said [I knew what was wrong], but also we had a lot of players injured, but it's my fault and I take all this."
However, Mancini refuted the suggestion that his tactical approach was to blame for the defeat, stating that his only ploy is to "run and score".
He added: "We changed for five minutes when we wanted to have one player in the hole. We changed only for five minutes, but on the pitch we are always 11 players.
"Before we conceded two goals. I don't think this is important. Three, four, five, six, seven. If someone wants to make this excuse, OK, but this is not important. When you play you should be strong: the tactic is one - run and score."
The 47-year-old went on to concede that City now face an uphill battle to qualify for the competition's knockout stages.
He continued: "I think that it is difficult [to qualify], very difficult. There are one team with seven [points], one with six, one with three. It should be a marathon like last year.
"I don't think [it will be difficult to recover]. We play football, we can play bad game like tonight, we can lose the game, but the season is long."