"I think Steve would have gone for the privacy," Wozniak told CNBC's "Power Lunch" on Thursday.
Cook on Wednesday denounced a court order requiring the tech giant to help authorities search an iPhone used by one of the attackers who killed 14 people in San Bernardino, California last year.
Cook called the order "chilling," saying the government could eventually use it to "extend this breach of privacy and demand that Apple build surveillance software" to gather personal data.
The disagreement reignited a tense debate about how much access technology companies should give to authorities and whether consumers should yield some privacy in the name of security. Many prominent Silicon Valley firms oppose a so-called "back door" through encryption for police, but numerous lawmakers have argued it is necessary to prevent further attacks.
The Department of Justice has maintained that the order would apply only to the phone in question.
Google CEO Sundar Pichai, among others, voiced support for Cook this week. In a tweet, he said "forcing companies to enable hacking could compromise users' privacy."
Wozniak noted that he was "not intimately involved in the fight." However, he said he might fight the order "quite vigilantly" if he had a say in it.
He said letting authorities crack one phone opens the possibility that they would seek a broader back door to Apple devices.
"I'm definitely against that. I don't think phones should have back doors," he said, adding that Apple would risk losing the trust that drives its brand loyalty.