Relations between Ankara and Riyadh have tightened considerably in the past months as they pursue joint interests in Syria. Erdogan had just the day earlier hosted Saudi Crown Prince Mohammed bin Nayef for talks at his palace.
"The allowing by the US Congress of lawsuits to be opened against Saudi Arabia over the 9/11 attacks is unfortunate," Erdogan said in a speech for the opening of parliament.
"It's against the principle of individual criminal responsibility for crimes. We expect this false step to be reversed as soon as possible," he added.
Families of 9/11 victims have campaigned for the law, convinced the Saudi government had a hand in the attacks that killed almost 3,000 people.
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Fifteen of the 19 hijackers were Saudi citizens, but no link to the government has been proven. The Saudi government denies any ties to the plotters.
Obama called the vote a "dangerous precedent" while Saudi Arabia warned it risked having "disastrous consequences".
The visit by the Saudi crown prince to Ankara was the latest sign of the burgeoning relationship between Turkey and Saudi Arabia, two mainly Sunni Muslim powers who both support rebels battling President Bashar al-Assad in Syria.
Erdogan told Nayef Friday that the expanding ties "offer opportunities for regional and global stability", the Anadolu news agency said. Nayef said Riyadh was pleased that the two countries "have the same thinking on all issues".
Erdogan also bestowed on Nayef Turkey's second highest state decoration for foreign nationals, the Order of the Republic.
The Turkish president earlier this year also backed Saudi Arabia in a diplomatic crisis with Iran over Riyadh's execution of prominent Shiite cleric Sheikh Nimr al-Nimr in January.