Blatter, who is suspended, is under criminal investigation over a payment made to European football federation head Michel Platini in 2011. Both men deny any wrongdoing.
“I don't think he should have ever stepped down. I don't think he should have been challenged. If people allegedly have been corrupted to make things happen in their country, it's good,” Ecclestone was quoted as saying by BBC on Friday.
The 85-year-old added, "It's a tax football had to pay." Ecclestone said the reason Blatter deserved support was "because of him we have a lot of countries around the world that are now playing football".
The 17-year FIFA reign of Swiss Blatter, who is suspended for 90 days, ends in February.
Ecclestone has run the commercial side of F1 for nearly 40 years and last year faced two separate trials on corruption charges.
Ecclestone also said that he believes nations and sport should be run by dictatorship.
"I don't think there's any place for democracy. Anywhere," the Briton said.
A civil case in the UK against Eccelestone was dismissed and he paid a German court 60 million pound to end a trial in which he was accused of paying a German banker 26 million pound to ensure a company Ecclestone favoured could buy a stake in F1.
But he has also helped F1 reach new venues like Sochi and Russia, where in the last weekend he witnessed the Grand Prix with President Vladimir Putin by his side.
Asked about Putin, Ecclestone said: "Super. I'm his best supporter."
And ahead of next weekend's American Grand Prix, Ecclestone said that he wants F1 to be in the United States only for a "little bit" and added that the country is not among the heavyweights anymore.
"They are a big island, so they are a bit isolated," he said. "They are slowly starting to learn what other people in the world do."
The US Grand Prix is in Austin, Texas, next weekend with Ecclestone expected to attend.