Crime scene investigators and other officials aided by sniffer dogs and a drone, first sealed off one of the villas in the Samanlı village of Yalova province and later expanded their search to the grounds of the neighboring villa.
The phone call was believed to be about the destruction or disappearance of the body parts, the prosecutor's office said.
A Tunisian journalists' union hung a large banner from its headquarters showing the prince holding a chainsaw - a reference to the dismemberment of Khashoggi's corpse. The latest searches came more than two weeks after pro-government Sabah daily reported that samples taken from the consulate drains showed traces of acid.
Khashoggi, a Saudi journalist and columnist for The Washington Post, went missing after entering the Saudi Consulate in Istanbul on October 2.
Investigators descended on the mansion and a neighbouring property in the province of Yalova, south of Istanbul, as part of their ongoing search for the body of the murdered Washington Post columnist.
Two policemen killed as gunmen attack Chinese consulate in Pakistan's Karachi
An armed separatist group that opposes China's economic presence in Pakistan has claimed responsibility for the attack. Police officials said the attackers fired weapons close to the consulate before hurling a hand grenade.
Turkey has maintained pressure on Saudi Arabia over the killing of the USA -based columnist for The Washington Post.
Yalova governor Muammer Erol told Anadolu in a written statement that the Istanbul public prosecutor in charge of the murder investigation would provide the "necessary information" about the results of the search later.
There is also no confirmation of who ordered the killing. Turkey has said he was killed by a 15-member Saudi hit squad and that his body was dismembered before being removed from the consulate.
The Saudi general prosecution said that its investigations revealed that a team was sent to Istanbul to persuade Khashoggi to return to the Kingdom. Khashoggi was a critic of Saudi Crown Prince Mohammed bin Salman.
Khashoggi was killed in a rogue operation and Saudi Arabia has since arrested several suspects in the case.