After an injury-ridden Asia Cup, 25-year-old Zaheer Khan was replaced by Ajit Agarkar in the squad announced on Thursday for the Holland tri-series, NatWest Challenge and ICC Champions Trophy.
Ganguly, who has always backed the Baroda paceman, said Zaheer was "not bowling well" and needed some time to get back his rhythm.
"When he is fit, he is the best bowler in the side. We are looking at the coming series at home against Australia and South Africa. We hope he gets back to his rhythm. He never looked very free in Asia Cup. We are looking at his future and that is the reason why he was not picked," said the skipper who was in New Delhi for a promotional campaign organised by LG.
But Ganguly denied that the left-arm pacer was played in the Asia Cup despite being not fully fit.
"When we picked him for Asia Cup, he was fit. He bowled everyday in the nets and did everything that is required to pass a fitness test.
"He bowled well in the first match against UAE in Asia Cup. But then in the next match, he pulled his quadriceps muscle -- it happened on the field. But he recovered from that injury and that is why we picked him (for the final)."
"He bowled well in that final over against Sri Lanka (in the last Super League match) and that is why we picked him for the final. But he did not bowl well in the final," Ganguly said.
The captain said he expected Zaheer to get back to his match-winning ways soon.
"He is a senior professional. We expect him to bowl well, he is one of our best bowlers," he said.
The skipper also defended his preference for going into a match with seven batsmen and said all top sides in the world have a similar combination.
"You have to see the number of games we have won while fielding seven batsmen. If you look at Australia they have Andrew Symonds coming at number seven, England have Andrew Flintoff. Pakistan have Abdul Razzaq. These are all batsmen who can bowl.
"We are also picking guys who can bat and bowl. Sehwag and Sachin bowled so well in Asia Cup. In fact Sachin was the second highest wicket-taker. If the pitch is seaming I will bowl ten overs."
In the same vein, Ganguly justified his decision to go into the Asia Cup final with three seamers although none of them went on to finish their quota of overs.
"Sri Lanka was the home team, they knew the conditions and they also went with three seamers. Sri Lankan batsmen are good players of spin and we wanted to get Sanath Jayasuriya out quickly. Also if one of the seamers did not do well, we could fall back on the third bowler.
"But we did not lose the final because of this. We lost because we did not bat well enough," he said.