Sopeaking on Wednesday at the European Union's privacy conference at the EU Parliament in Brussels, Cook said that customer data was being "weaponized with military efficiency" by companies to increase profit.
Apple, which designs many of its products so that it cannot see users' data, has largely avoided the data privacy scandals that have enmeshed its rivals Google and Facebook this year.
"The desire to put profits over privacy is nothing new," Cook said.
He cited former U.S. Supreme Court Justice Louis Brandeis who in a Harvard Law Review article in 1890 warned that gossip was no longer the resource of the idle and the vicious but had become a trade.
"Today that trade has exploded into a data industrial complex. Our own information, from the everyday to the deeply personal, is being weaponized against us with military efficiency," he said.
"These scraps of data ... each one harmless enough on its own ... are carefully assembled, synthesized, traded, and sold."
He said algorithms were turning harmless preferences into hardened convictions.
"If green is your favorite color, you may find yourself reading a lot of articles - or watching a lot of videos - about the insidious threat from people who like orange," Cook said.
Cook also warned about governments abusing users' data and their trust, a concern for many with elections coming up in several countries worldwide.
"Platforms and algorithms that promised to improve our lives can actually magnify our worst human tendencies," Cook said.
Cook said Apple fully backed a federal privacy law in the United States, something Europe has already introduced via its General Data Protection Regulation.