Duda said he was sending amendments to parliament because he was aware of the domestic and international criticism surrounding the law proposed by Poland's governing conservative Law and Justice (PiS) party.
The president said his amendments aimed to ensure that the probe is conducted by nonpartisan experts and that their findings would not ban anyone from holding public office.
He said he was also strengthening the right to appeal before a court for those under investigation.
The president's announcement came after he said on Monday that he had approved a law establishing a special panel to investigate Russian influence in Polish politics.
Duda approved the measure after it passed parliament last Friday on a final vote of 234 to 219, with one abstention, Polish state news agency PAP reported.
The president, who is an ally of Poland's conservative government, told reporters at the time that he had "no doubt that the issue of Russian influence needs explaining."
The US State Department and the European Union have since expressed concerns about the Polish law, which has caused a public outcry.
Critics have said it violates the Polish constitution and could keep government opponents from holding public office and block opposition candidates in an election due in the autumn, the AP news agency reported.
Polish opposition politicians said last week that the proposed probe was specifically targeted at former Prime Minister Donald Tusk, who is the leader of the country's largest opposition grouping, the Civic Coalition.
A spokesman for the country's ruling conservatives said on Wednesday that the new commission to investigate Russian influence in Poland could be appointed at the next session of parliament on June 9.
Friday is day 464 of Russia’s war on Ukraine.
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Source: IAR, PAP, AP, TVP Info