"These are fabricated reports released by ill-wishers standing behind the scene," Gumrukcu told reporters in a press conference at the Turkish embassy in Tehran on Tuesday.
"Those who want to damage Turkey's relations with other countries pursue such subjects," he added.
Gumrukcu underlined that despite some differences with the neighboring states, including Iran, on the Syrian crisis, Turkey will never allow Israel to access its military bases for attacking other countries.
"Differences have existed at different periods in the relations between Iran and Turkey since long time ago, but these differences have never hurt the main core of the two countries' good relations, as the two countries' relations are expanding despite some differences," he stressed.
Tehran and Ankara have recently expanded their bilateral relations, especially in trade and energy fields. Trade between Turkey and Iran has risen sharply over the past decade. Iran-Turkey trade value exceeded $22bln in 2012.
Also, Turkey was Iran's fifth-largest oil customer in 2011, buying around 200,000 barrels per day, 30 percent of its total imports and more than 7 percent of Iran's oil exports.
The two countries officials stressed the necessity for stronger relations and pursuing the planned increase of mutual trade to $30bln by 2015.