"Let me say it clearly; a presidential system does not mean federations," Yildirim told a meeting of the ruling Justice and Development (AK) Party in Istanbul.
He said Turkey’s presidential model would be based on the principle of "one nation, one country, one flag, and one state."
Yildirim also denied claims that the new system would result in division within the country.
The government has long sought to replace the current parliamentary system with a presidential one, saying there are flaws in the system that hold back Turkey’s development.
Last week, Yildirim said a committee within the AK Party had completed work on a draft constitution that also includes items for a presidential system.
The proposed changes would be put to a public referendum even if the government gets the necessary votes in parliament to avoid the need for one, Yildirim said.
"The will of the people is above all," he stressed.
Stating that the AK Party lacks the votes to pass the bill in parliament single-handedly, he asked the opposition Republican People's Party (CHP) and Nationalist Movement Party (MHP) to support efforts for a new constitution including the presidential system.
"We want to see as much participation and reconciliation [in the process]," he added.
He reiterated that the bill would be submitted to parliament "very soon."