The institute plans to release the documents next month, Poland Radio reported. Janusz Kurtyka, the head of the institute, says Kwasniewski appears in the files of the Intelligence of Socialist Poland with the code name Alek.
Kwasniewski, who served as president from 1995 to 2005 after defeating Lech Walesa, denies working with Communist spy agencies. He has accused the institute of a political feud.
"I know who I am and who I was. I was never a secret agent registered as 'Alek' or under any other codename and this has already been proven," the former president said.
The Lustration Court, set up to vet officials, determined in 2000 that Kwasniewski had not worked with the secret service. Kwasniewski was sports minister under the Communist government in the 1980s and became a leader of a social democratic party in the post-Communist era.