His statements directly contradict those of moderate Iranian President Hassan Rouhani, who says his government is ready to hold talks with the U.S. on how to resolve the conflict in Syria, where the two countries back opposing sides.
"Negotiations with the United States open gates to their economic, cultural, political and security influence. Even during the nuclear negotiations they tried to harm our national interests," Khamenei was quoted as saying on his website. "Our negotiators were vigilant but the Americans took advantage of a few chances."
Although he supported the last 18 months of negotiations, Khamenei has not publicly endorsed the nuclear agreement with the U.S., Germany, France, Britain, China and Russia that settled a standoff of more than a decade.
The West feared Iran wanted to develop nuclear weapons, suspicions Tehran denies.
The agreement, which curbs Iran's nuclear program in exchange for the lifting of crippling sanctions, was welcomed by Iranians who are keen to see their living standards improve and better relations with the rest of the world.
It was also a great political victory for Rouhani and his faction in Iran ahead of some key elections next year and as such has deepened the divide in Iran's complex power structure between moderates and hardliners.
In his address to Revolutionary Guards Navy commanders, Khamenei said talks with the U.S. brought only disadvantages to Iran.
"Through negotiations Americans seek to influence Iran...but there are naive people in Iran who don't understand this," Khamenei was quoted as saying to the IRGC commanders, who are also running much of Iran's military involvement in Syria.