It comes after the Facebook boss said that the doomsday scenario put forward by Mr Musk was unhelpful.
Mr Musk tweeted: "I've talked to Mark about this. His understanding of the subject is limited."
The pair represent two distinct groups, those saying AI's benefits will outweigh its negatives and those saying it could ultimately destroy humanity.
Mr Zuckerberg's comments were made as part of an informal Facebook Live chat, aired during a barbecue at his Palo Alto home.