"Airlines are permitted to find that any specific animal, regardless of breed, poses a direct threat," according to the agency.
The DOT said that after its guidance document is officially published next week, airlines will have 30 days to comply.
But it's yet to be seen if Delta will change its policy to comply.
The DOT in its document released Thursday says conforming with the guidance “is voluntary only” and that its guidance “is not legally binding in its own right and will not be relied on by the Department as a separate basis for affirmative enforcement or other administrative penalty.”
Delta issued a statement saying it "continuously reviews and enhances its policies and procedures for animals onboard as part of its commitment to health, safety and protecting the rights of customers with disabilities."
The airline said its change in policies last year was "to reinforce our core value of putting safety and people first, always."
Another Delta policy limiting emotional support animals on long flights also does not conform with the DOT's new guidance.
The DOT said airlines should not automatically prohibit service animals or emotional support animals on flights lasting eight or more hours.
But Delta's policy today is that passengers may not bring emotional support animals on flights longer than eight hours.
Delta made that change to its policies after saying it carries 700 service or support animals a day and had seen an 84 percent increase in incidents involving service and support animals in 2016 and 2017, "including urination/defecation, biting" and a mauling by a 70-pound dog that led to a lawsuit against the airline and the dog's owner.
Industry group Airlines for America issued a statement saying more than 1 million passengers brought emotional support animals on flights last year, and it saw a “sharp increase in incidents such as biting and mauling by untrained animals.”
"The availability of fraudulent ESA [emotional support animal] credentials online has enabled people who are not truly in need of animal assistance to abuse the rules and evade airline policies regarding animals in the cabin," Airlines for America said.
The Association of Flight Attendants union issued a statement saying flight attendants “have been hurt and safety has been compromised by untrained animals loose in the cabin.”
Fraudulent claims of emotional support animals threaten safety and can affect the rights of passengers “who legitimately need the assistance of trained animals,” according to the flight attendants union, which added that there is “a mess of animals loose in the aircraft cabin.”