Erdogan had told journalists travelling with him to Iran that the country's nuclear programme, which Western nations say could be a cover for building weapons,
"is an energy project with peaceful, humanitarian purposes".
"If their [Iran's] positive attitude is answered with a positive attitude, this will bring forward the process in the positive direction"
Recep Tayyip Erdogan,
Turkey's prime minister
He said talks between Tehran and world powers in Geneva on October 1 showed that it "can work with" the United States and Russia on uranium enrichment.
"If their positive attitude is answered with a positive attitude, this will bring forward the process in the positive direction," Erdogan said.
His latest remarks came after an interview in Britain's The Guardian newspaper in which he accused Western powers of treating Iran unfairly and referred to Ahmadinejad as a "friend".
Ties between Israel and Turkey have deteriorated since the December-January war on Gaza.
Ankara had previously attempted to mediate relations between Israel and other Middle Eastern nations, but earlier this month, Turkey banned Israel from an international air exercise because of the Gaza conflict.
The Turkish prime minister has brought a 200-member delegation, comprising ministers, members of parliament and business leaders, to Iran to discuss a wide range of bilateral, regional and international issues.
Isna, the Iranian students news agency, said that Ahmadinejad had told Erdogan there were no limitations to Iranian-Turkish co-operation.
Taner Yildiz, Turkey's energy minister, said that one of the areas in which the two neighbours would work together was gas exploration.
He said that Turkey would start exploration work at Iran's South Pars gas field next month as part of a project to sell gas to Europe, the state-run Anatolian news agency reported.
"Turkish Petroleum will be exploring in the South Pars Field ... The work will have started by the first or second week of November," Yildiz said.
It was not immediately clear whether the gas would go through the planned $11.76bn European Union-backed Nabucco pipeline, which was agreed with ankara in July.
Erdogan on Tuesday said he supported Iran's presence in the Nabucco project and added: "I believe that sooner or later, the project will understand the importance of Iran's participation".
Iranian-Turkish trade stands at around $12bn a year and the two nations are seeking to expand it to $20bn in the next two years.
Erdogan is also expected to hold talks with Ayatollah Ali Khamenei, Iran's supreme leader and Ali Larijani, the parliamentary speaker during, his visit.