Iran "has no trust in America and will not in any way repeat the bitter experience of the previous negotiations with America," Khamenei said in comments published by his official website.
They came after he met with Japan´s Prime Minister Shinzo Abe making an unprecedented visit to Iran -- the first by a Japanese premier since the 1979 Islamic Revolution.
"We have no doubt in your good will and seriousness, but regarding what you said the US president told you, I don´t consider Trump as a person worthy of exchanging messages with," Khamenei told Abe during their meeting.
The visit coincided with a suspected attack on two oil tankers in the Sea of Oman, off the Iranian coast, with one of the ships owned by a Japanese company, which again sent tensions in the Gulf soaring.
Iran has been locked in a bitter standoff with the United States since Trump withdrew from a landmark 2015 nuclear deal in May last year.
"President Trump has said he does not wish to see an escalation of tensions," Abe told reporters after his meeting.
"I shared candidly with Ayatollah Khamenei my own views about what intention the president has in mind," Abe said, emphasising he had "exchanged views with President Trump several times".
Trump indicated last week in France that he could consider talking to Tehran, saying: "I understand they want to talk and if they want to talk that´s fine."
Abe said he believed his meeting with Khamenei was "a significant step forward" for "securing peace and stability of this region."
During a news conference with Abe on Wednesday, President Hassan Rouhani said he expected a "very positive change" in the Middle East and the world if the United States stopped what he called its "economic war" on Iran through sanctions.
