"My view is that's not an appropriate way for a presidential candidate to behave," Bezos said at an event held by The Washington Post, the newspaper he owns.
Trump, the billionaire businessman, told Fox News last week that Amazon has "a huge antitrust problem." He accused Bezos of using the Post as a "toy" to help Amazon, the world's largest online retailer, get fair treatment from politicians.
"Amazon is getting away with murder tax-wise. He's using The Washington Post for power so that the politicians in Washington don't tax Amazon like they should be taxed," Trump contended.
Bezos responded by saying he is "very, very comfortable with all of Amazon's approaches and behaviors."
"The way we pay taxes, the political positions we take, are focused on our business and very appropriate," he said.
Bezos also addressed Amazon's Fire Phone, which the company stopped selling last year after seeing lackluster demand.
He said: "We're working on much bigger failures right now. Some of them are going to make the Fire Phone look like a little blip."
— CNBC's Karen Stern contributed to this report.