A consolation place in the knockout stages of Europe's second-tier competition is now the best City can hope for from their disappointing Champions League campaign.
The Barclays Premier League champions have failed to win any of their first five Group D matches and will bow out of the tournament after their final match against Borussia Dortmund on Tuesday.
Even finishing third in the group will be a tough task. City will need to beat the group winners in Germany and hope Real Madrid, also already through to the last 16, can do them a favour against Ajax.
Mancini said: "Yes, we want to stay in the Europa League - this is normal.
"It is another competition, another trophy to try to win.
"Maybe when it starts in February it is not so important and could be a problem because we play more games, but if you arrive in the semi-final or the final it becomes an important competition for us. And for this reason we want to stay in Europe."
Mancini knows the club owners have been disappointed by the Champions League failure but remains confident of delivering a successful season.
The Italian has spoken to chairman Khaldoon Al Mubarak about the situation.
Mancini said: "He is happy with the way we are going in the Premier League, and we have the FA cup to come.
"Obviously they (owners) are so disappointed about the Champions League, and this is normal because our target when we started the competition was to get to the knockout stage - and anything can happen when you arrive there.
"But we didn't do well and for this reason I think they are disappointed but they understand it takes time to succeed in the Champions League."
It is City's second successive failure in the Champions League but Mancini feels he need look no further than this week's opponents for inspiration.
German champions Dortmund also crashed out at the group stage last year but have been inspired this time around.
He said: "Last season, for instance, Borussia Dortmund went out at the group stage with only four points.
"But this season they are looking like one of the teams who can win the competition.
"One year can change everything. We made some mistakes on the pitch but this is the Champions League."