Jony Ive appeared to attack the Moto Maker scheme in an interview in which he criticised the idea of giving consumers huge choice over how their handsets were made to appear.
Rick Osterloh, president of Motorola, told the BBC his company had a "different philosophy".
And he criticised Apple in turn, calling its prices "outrageous".
Sir Jonathan specifically asked the New Yorker magazine not to name the company he had been "scathing about", but a campaign launched by Motorola in late 2013 matches the description he gave.
"Their value proposition was, 'Make it whatever you want. You can choose whatever colour you want,'" Sir Jonathan is quoted as saying.
"And I believe that's abdicating your responsibility as a designer."
Motorola promotes Moto Maker as offering shoppers "thousands of ways" to customise its Android-powered Moto X handsets. Choices include the colour of the model's back, the type of metal trim used and the option to include a variety of leathers in its design.Moto Maker allows shoppers to customise the colours and finish of their smartphone
Mr Osterloh of the scheme: "Our belief is that the end user should be directly involved in the process of designing products.
"We're making the entire product line accessible.
"And frankly, we're taking a directly opposite approach to them [Apple]."
He added that he believed this difference in strategy went wider than design.
"We do see a real dichotomy in this marketplace, where you've got people like Apple making so much money and charging such outrageous prices. We think that's not the future," he said.
"We believe the future is in offering similar experiences and great consumer choice at accessible prices.
"The mobile phone industry's greatest failure is also its greatest opportunity: to make really good, affordable devices for people who don't want to spend a lot of money.
"A great smartphone, and a great mobile internet experience, shouldn't be an expensive luxury. It should be a simple choice for everyone."Mr Osterloh said Apple's prices were "outrageous"
Motorola launched Moto Maker while owned by Google, but it has since become a division of China's Lenovo.'Insipid' cars
Sir Jonathan - who was knighted in 2012 for his services to design - was also critical of another brand, in the New Yorker article, suggesting Toyota's Echo model was "shocking".
"It is baffling, isn't it? It's just nothing, isn't it? It's just insipid," he said of the vehicle, which is also sold as the Yaris.
A spokeswoman for Toyota declined to comment.
Sir Jonathan did, however, praise Bentley's vehicles, saying he "loved" their designs.
According to reports by the Financial Times and the Wall Street Journal, Apple is working on a car as a possible follow-up to its forthcoming smartwatch.