“We support the diplomatic initiative of the government and attach importance to its activities in this trip,” he said on his website.
But he added that some of what had occurred “was not appropriate”.
Mr Rouhani had spoken to US President Barack Obama by phone in a bid to ease tension over Iran’s nuclear programme.
They were the first talks between Iranian and US leaders in more than three decades.
Some of what happened on the New York trip was not appropriate”
Ayatollah Ali Khamenei
Iran wants the lifting of UN sanctions, which were imposed over concerns that it is seeking to build nuclear weapons clandestinely – an allegation Tehran denies.
Israeli Prime Minister Benjamin Netanyahu, the leading advocate of a hard line against Iran over its nuclear programme, has dismissed Mr Rouhani as a “wolf in sheep’s clothing”.
‘No trust’When Mr Rouhani returned from New York he was greeted at Tehran airport by hardline protesters chanting “Death to America”.
BBC World Affairs Editor John Simpson explained Ayatollah Khamenei’s hold on power during the election in June
In his comments on Saturday, Ayatollah Khamenei said that “some of what happened on the New York trip was not appropriate”, without being specific.
“We are pessimistic towards the Americans and do not put any trust in them,” he said.
“The American government is untrustworthy, supercilious and unreasonable, and breaks its promises.”
Substantive nuclear negotiations between Iran and international powers are due to take place on 15 October and Mr Rouhani has promised to bring a plan to the meeting.
He said he wanted to reach a deal over the nuclear issue in three to six months.
Iran’s key nuclear sites
- Netanyahu: I’m prepared to talk to Rouhani on phone… (telegraph.co.uk)
- Iran parliament endorses Rouhani’s diplomatic outreach (dailystar.com.lb)
- Khamenei says part of diplomatic push in NY ‘not proper’ (dailystar.com.lb)
- Netanyahu: Khamenei Rules Iran, Not Rouhani (israelnationalnews.com)