Ankara is concerned that the focus of the US-led coalition on fighting IS extremists will take attention away from Turkey's long-standing aim of toppling the Syrian leader.
In a speech to the thousands of supporters in the Black Sea city of Trabzon, Erdogan said the Assad regime and IS were both terror groups who should be dealt with accordingly.
"We cannot leave their fate into the hands of the murderer Assad who is waging a state terror," said Erdogan, referring to the 1.5 million Syrian refugees that Turkey has taken in during the conflict.
"We have always displayed a principled stance towards all terrorist organisations. We are not discriminating against terror organisations, saying this one is good or this one is bad," he said in the televised speech.
"We have adopted the same stance towards ISIS," he said using a variant of the name for IS. "But other terrorist organisations pose a threat to us too."
Ankara has vehemently opposed Assad during the three-and-a-half-year Syria conflict but has been criticised for not showing greater involvement in the fight against IS extremists.
Earlier, Prime Minister Ahmet Davutoglu said: "Turkey is against ISIS just the same way that it is against Assad."
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"Assad and ISIS are both responsible for all these events and tragedies," he told reporters in Ankara.
He added: "No one can prove that Turkey is supporting ISIS."
Turkey has been reluctant to intervene militarily against IS jihadists trying to take the mainly Kurdish town of Kobane just across the border, despite having parliamentary authorisation for military action in Syria.
Ankara has been accused of encouraging the rise of IS with its support for Islamist-tinted rebel groups in Syria seeking to oust Assad and is now seeking a commitment from the West to move against the Syrian leader.
Davutoglu ridiculed Turkey's main opposition leader Kemal Kilicdaroglu, who suggested that parliament should issue a separate mandate for Turkish military action in Kobane.
"Are we going to issue a separate mandate for each province or district? It's such a ridiculous proposal," Davutoglu scoffed.