The Iranian embassy has rejected and denounced what it said were baseless allegations made by the Bangkok Post about Iran and its citizens.
It follows the publication of a story in which police were told to be on the lookout for Iranian spies in the country.
The embassy said it has pursued the issue through diplomatic channels. So far, no Thai political or security officials have confirmed the claim, it said.
The embassy said it reiterated that historical and friendly relations between the Islamic Republic of Iran and the Kingdom of Thailand have always been based on mutual understanding and respect.
Since the Islamic Revolution, Iran has been subject to such smear campaigns while paying a high price fighting terrorism, including defeating Isis, according to the embassy.
In recent days, with the aim of influencing negotiations on Iran's peaceful nuclear programme, which is fully monitored by the IAEA, Israeli and certain Western media have published bogus allegations about Iran, the embassy claimed.
Iran, with its unique experiences and good record in fighting terrorism, has offered cooperation in this regard to friendly countries including the kingdom of Thailand, it said.
The embassy said it considers the publication of such baseless allegations as fake and disinformation, aiming at damaging Iran and the historical and friendly relations between Tehran and Bangkok.
"The embassy will continue its efforts in boosting our bilateral relationship for the common interests of our two nations," it said.
A source at the Royal Thai Police (RTP) previously told the Bangkok Post that RTP had issued a secret order to police nationwide to keep an eye out for spies alleged to be from Iran after one was arrested in Indonesia.
The order cited an incident on May 27, last year when Indonesian authorities arrested a man named Ghassem Saberi Gilchalan carrying a fake Bulgarian passport at Soekarno–Hatta International Airport just before he departed for Qatar, the source told the newspaper.
Indonesian police found that he entered the country more than 10 times using fake passports and a court sentenced him to two years in jail for the offences, the source said.
Pol Maj Gen Khemarin Hatsasiri, head of the RTP's foreign affairs division, on Wednesday also denied the news media report, saying the RTP did not issue an alert about anyone from Iran.
After verification with the RTP and security agencies, the Foreign Affairs Ministry on Wednesday similarly rejected the report, and insisted Thailand and Iran have enjoyed amicable relations and respect for each other, despite the media claim.