After being warned about his conduct by Ferrari president Luca di Montezemolo in July, Alonso was then the subject of public overtures from McLaren on a weekend it emerged he was also a possible candidate for the second 2014 Red Bull seat.
Ecclestone believes Alonso was keen to move, and that his form suffered as a result.
While the two-time world champion ended the year as Sebastian Vettel's nearest challenger, he surrendered 116 points to the German over the final nine events.
Alonso was also outqualified by team-mate Felipe Massa five times over the final eight races.
"I've been a little disappointed in Fernando, because I'm a big supporter of him and Ferrari," Ecclestone wrote in a foreword to the official Formula 1 season review.
"I thought he gave up a little bit, which is proof he was looking for another team."
Alonso and Ferrari: an act of war or the art of war?
Ecclestone said he was also unsure whether Ferrari could provide Alonso with a championship-winning car, adding: "I don't know whether the team is not competitive because of him or because the people running the team aren't getting the job done.
"He certainly deserves a car that's capable of winning races. Whether that Ferrari is or not, I don't know."