The announcement on Instagram late on Monday by Zarif, the lead negotiator of Iran's landmark 2015 nuclear deal with major powers, prompted reports that large numbers of diplomats were considering resigning too in a show of support.
But in comments to ministry staff on Tuesday, Zarif said: "I advise all you dear brothers and sisters in the foreign ministry and embassies to resolutely follow your duties in defence of the country and refrain from such acts."
The official IRNA news agency said Zarif had also commented for the first time on the reason for his announcement.
Architect of nuclear deal, Iran's Foreign Minister Zarif resigns
"I hope my resignation will act as a spur for the foreign ministry to regain its proper statutory tole in the conduct of foreign affairs," it quoted him as saying.
There was no immediate indication President President Hassan Rouhani had accepted the resignation and a petition urging him not to was signed by a majority of members of parliament, senior lawmakers said.
According to Iran's Entekhab news agency, Zarif's resignation appears to be linked to a surprise visit by Syrian President Bashar Al Assad to Tehran on Monday.
The top diplomat was not present at any of the meetings Assad had with the Supreme Leader Ayatollah Ali Khamenei and Rouhani, according to semi-official news agency ISNA.
Entekhab said it tried to reach Zarif and received the following message: "After the photos of today's meetings, Javad Zarif no longer has any credibility in the world as the foreign minister!"
As the lead negotiator in the nuclear deal, Zarif's standing within Iran's political establishment took a hit when the US withdrew from it and reimposed crippling unilateral sanctions last year.
Ultra-conservative MPs tried to impeach him, only backing down in December as the initiative lost steam.
Zarif said his main concern throughout the negotiations for the nuclear deal had been about pressure from inside Iran.
In an interview with Jomhoori Eslami newspaper published on Tuesday, he said partisan disputes over foreign policy were 'a deadly poison.'
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