The Turkish leader and head of the Roman Catholic Church have both strongly opposed the move announced by US President Donald Trump, and Erdogan has called an emergency summit meeting of the Organisation of Islamic Cooperation (OIC) on December 13.
The state-run Anadolu news agency gave no further details but NTV television said Erdogan and Francis shared their concern over the situation.
Citing presidential sources, it said that Erdogan expressed his appreciation to Francis for his stance on the issue and both agreed the status quo should not be changed.
Last year, Turkey and Israel ended a rift triggered by Israel´s storming in 2010 of a Gaza-bound ship that left 10 Turkish activists dead and led to a downgrading of diplomatic ties.
The two sides have since stepped up cooperation, particularly in energy, but Erdogan, who regards himself as a champion of the Palestinian cause, is still often bitterly critical of Israeli policy.
Erdogan earlier warned Trump that the move would put the region in a “ring of fire”.