"In Geneva 2, we must make sure that... all the measures will not fail...so that we can (bring) in an era without Bashar al-Assad," he said, referring to peace talks planned later this month in Switzerland.
The Syrian conflict is estimated to have claimed more than 130,000 lives, and has forced millions more to flee their homes.
"A person who has allowed that to happen still remaining at the top of the country cannot be accepted," Erdogan said.
UN leader Ban Ki-moon has started sending out invitations to the so-called Geneva 2 peace talks, but Assad's key ally Iran was not on the first list, UN deputy spokesman Farhan Haq said.
That could help pave the way for the opposition National Coalition, which has repeatedly stipulated that Iran must not be invited, to participate.
The 30 countries invited to the Geneva talks include Saudi Arabia, a major backer of the Syrian opposition, as well as the five UN Security Council permanent members -- and Syria's neighbours Turkey, Iraq and Jordan.
Japan's foreign minister Fumio Kishida is also expected to attend.
"In the Geneva 1 there were several issues that were taken up and in the Geneva 2 we will make sure that these will not fail.... It is very important that Japan takes part in this," Erdogan said.
The Coalition, which re-elected Ahmad Jarba as its leader on Sunday, will discuss Tuesday whether to attend the talks, although a key group -- the Syrian National Council -- has already announced a boycott.
US Secretary of State John Kerry and Russian Foreign Minister Sergei Lavrov will meet on January 13 in a bid to decide Iran's role in ending the nearly three-year-old war, said Haq.
Erdogan is on a three-day visit to Japan, with more than 100 business officials, aimed at boosting economic ties with Tokyo. He will also visit Malaysia and Singapore.
He was speaking at lecture hosted by the Nikkei newspaper and the Turkish embassy in Japan, and did not address the current political machinations at home, where a corruption and bribery investigation has shaken his pro-business government.