Smith is not part of Australia's three-man selection panel, but he has been assailed by former players who believe he gets too much say in Australia's lineups.
The captain hit back strongly at a media conference in Sydney, calling suggestions of favouritism "absolute garbage".
"I'm not a selector, but I certainly speak to the selectors a lot and express my views," Smith told reporters.
"All this rubbish about me picking my mates, it's absolute garbage. I certainly don't agree with that."
Blues coach Trent Johnston said it was one of the toughest decisions of his coaching career to leave out the former Test opener, who was the top run-scorer in last season's Sheffield Shield.
Cowan told Fox Sports: "I don't agree with that selection policy, but it's the Australian Test captain, it's his team."
This prompted criticism from former Test paceman Rodney Hogg, among others, of Smith's alleged "captain's calls" at the selection table.
"People can say what they like," the 28-year-old said. "I'll read it, but it doesn't bother me. I'll just get on with it."
England begin their tour in a two-day hit-out against a WA XI in Perth, starting on Saturday, in the build-up to the first Ashes Test in Brisbane on November 23.
Smith rates the Ashes battle with Joe Root's tourists as the biggest challenge he's faced as Australia captain.
"No doubt. Ashes series are always big," Smith said. "This is my first Ashes series as captain and it's going to be a good challenge."
Smith, who has a batting average of 59.66 from 56 Tests with 20 centuries, hasn't started the new domestic season in great scoring shape either. But he said he hopes things are now coming together.
"I haven't felt great for a little while now," he said.
"I think I've made some progress the last couple of days. It'll be good to spend some time in the middle to just reaffirm that.
"Had a really good hit today, felt like I figured things out at the end.
Disclaimer: No Business Standard Journalist was involved in creation of this content
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