The government bill had proposed shutting down the CBA from 1 October, with its powers transferred to the police, the internal security agency ABW and the National Revenue Administration.
In a video statement, Nawrocki said the CBA was "the first service built from scratch in free Poland" and unconnected to the communist-era security apparatus.
Abolishing it, he argued, would create a "competence chaos", disrupt ongoing investigations and drive out experienced officers.
That expertise, he said, had taken 20 years to build and could not be replaced within months.
The president added that even experts from the Batory Foundation – an organisation considered close to the current governing coalition – had noted the law lacked any overarching anti-corruption strategy.
The spokesman for the minister coordinating the security services, Jacek Dobrzyński, hit back, saying the president had acted "against the will of the Sejm [lower house ed.], the Senate and public expectations".
He said the government would now work on revised legislation to preserve reforms aimed at keeping the CBA free from political interference, including strengthening the legal independence of its chief.
Abolishing the CBA was a commitment in the coalition agreement of Prime Minister Donald Tusk's government.
The agency, which marks its 20th anniversary this year, was established as a flagship policy of the Law and Justice party (PiS), with which Nawrocki is closely allied.
The CBA's first head was Mariusz Kamiński, convicted of abuse of power and later pardoned by former President Andrzej Duda.
(ał)
Source: PAP