His comments came as US Secretary of State John Kerry met Iranian counterpart Mohammad Javad Zarif for a second time on the sidelines of a security conference in Germany, to ratchet up efforts for a lasting nuclear accord.
"I agree with a deal that can take place but I do not agree with a bad deal," the Iranian leader said, according to the Khamenei.Ir website.
"The Americans keep reiterating that it's better to have no deal than a bad one. I fully agree with that," he told air force commanders.
Khamenei, who has the final word on all matters of state in Iran, leaves the day-to-day administration of policy to President Hassan Rouhani and his government, but periodically speaks out on the nuclear talks.
Rouhani has made the lifting of Western sanctions imposed over Iran's nuclear programme his government's top priority.
But Khamenei has set "red lines" for the concessions that Rouhani can make.
These include a much bigger uranium enrichment programme than Western governments have said they are willing to countenance as they seek to allay concerns about any military dimension to Iran's nuclear activities.
"I don't go along with this talk of striking a deal on general principles first and an agreement on the details afterwards... If they're going to strike a deal, let them agree the principles and the details at the same time."
Zarif echoed Khamenei's comments after meeting Kerry in Munich today.
"I don't think if we don't have an agreement it will be the end of the world. We try, we fail," he said.
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