In addition to the search of the villas, security agents, using sniffer dogs and drones, drained a well in the yard of one of the houses.
Khashoggi, a Washington Post contributor who had written columns critical of current Saudi leaders, was killed inside the Saudi Consulate in Istanbul on October 2 by members of a 15-man team that had been sent to Turkey from Saudi Arabia, according to Turkish and Saudi prosecutors.
The news outlet, without citing a source, said the villas belong to two Saudi businessmen, including one who had allegedly been contacted by phone by some members of the 15-man Saudi assassination squad that traveled to Istanbul to carry out the deadly operation.
Turkish President Recep Tayyip Erdogan said in a speech last month that members of the Saudi team travelled to Yalova one day before the killing in an apparent search for a spot to hide the body.
Photographs of the raid showed police officers standing in front of a grand two-story villa surrounded by woods.
Saudi Arabia has insisted that the prince was not involved in the killing but U.S. senators have said they believe he was responsible.
Meanwhile, Prince Mohammed was due to arrive in Egypt on Monday for a two-day visit, state news agency MENA reported, part of his first trip overseas since Khashoggi's murder.
Intelligence officials in several Western countries say the killing was nearly certainly carried out with either the authorization or knowledge of Saudi Crown Prince Mohammed bin Salman, the kingdom's de facto ruler.
Irfan Fidan, chief prosecutor for Istanbul who heads the investigation into Khashoggi, ordered the search of the mansion, some 60 miles from Istanbul.
Saudi Arabia initially said Khashoggi had walked out of the consulate before shifting its account of what happened amid Turkish intelligence leaks.
His body has not been found and his death has triggered widespread global criticism of Saudi Arabia.
Investigators widened their search to Yalova and Belgrade forest on the outskirts of Istanbul for the remains of the journalist.