Ahmadinejad also described ties between Tehran and Doha as "brotherly and excellent," state television reported.
"Cooperation between Iran and Qatar can guarantee security and stability in the region," the emir was quoted as saying.
It was the first visit by an Arab leader to the Islamic republic since US diplomatic memos from Arab countries in the Gulf were released by whistleblower WikiLeaks late last month, uncovering a fixation on the Iranian nuclear threat.
According to a leaked memo Saudi King Abdullah had repeatedly pressed the United States to attack Iran to halt its nuclear programme, saying the US should "cut off the head of the snake."
But another leaked memo revealed that Sheikh Hamad had dismissed the threats of proliferation, saying they were made only to scare Iran.
Iran insists its nuclear programme is entirely peaceful, but world powers suspect Tehran is working toward an atom bomb.
In a meeting with the emir, Iran's supreme leader Ayatollah Ali Khamenei said that all countries in the region would lose if security were undermined, the official IRNA news agency reported.
"Unfortunately, the Americans and Zionists fuel these countries' ignorance of the importance of security in the region," Khamenei said without naming any countries.
"If the security of the region is hurt all of its countries will be unsafe, and lose," he warned.
Meanwhile on Monday a group of Iranian Revolutionary Guards navy commanders and forces headed to Qatar on five warships for a three-day visit to its military centres, IRNA reported.
Deputy head of the Revolutionary Guards' navy, Alireza Tangsiri, said the visit came at the invitation of Qatar after its military officials participated in Iranian wargames this year.
"Such programmes will definitely pave the way for mutual cooperation," he was quoted as saying by the agency.
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