"He went missing after three days stay in Turkey. Police inquiries show he has not left Turkey," he said, adding there was no indication Asgari had died or had been hospitalised.
Turkish media reports said Asgari, 63, went missing after checking into an Istanbul hotel on February 7.
Israeli media have speculated that their secret service might be involved in the disappearance of Asgari, who served under Mohammad Khatami, Iran's reformist former president.
Gad Shimron, a journalist with the Israeli newspaper Maariv and a former agent with the Mossad foreign intelligence agency, said Asgari was a former senior official with Iran's elite Revolutionary Guards who had access to information on the country's controversial nuclear programme.
Israeli army radio also said that during his time in Lebanon, Asgari was also Iran's liaison with the Lebanese Hezbollah group and "other terrorist groups".
Asgari was also reportedly in charge of "special missions" carried out by the Revolutionary Guards in Lebanon in 1986, when Israeli airman Ron Arad went missing after ejecting from his plane over the south of the country, the Israeli media said.
Israel has long said that Iran is responsible for his disappearance.
Iran asks for help
The Iranian government said it was sending a team to Istanbul to search for Asgari and called on Turkey to provide all necessary assistance.
"Mr Asgari disappeared during a recent trip to Turkey and the foreign ministry is following the affair, most notably by sending a consular mission," Manouchehr Mottaki, the Iranian foreign minister, told reporters.
"Iran is demanding explanations from the Turkish authorities."
No official indications of Asgari's whereabouts or the reasons for his sudden disappearance have been given.
The Turkish government has not publicly commented on the case.