Vil Mirzayanov was involved in the secret Soviet program in creating the nerve agent, and was the first to reveal Novichok’s development.
In an interview with Russia’s TV Rain on Saturday evening, the chemist said he wanted to apologize to Navalny after Germany said it found "unequivocal evidence" he was poisoned with Novichok.
The opposition politician on Saturday described his severe symptoms after falling ill on a plane on August 20, including the inability to form words, saying he still struggled to pour a glass of water or use a phone.
"I offer my profound apologies to Navalny for the fact that I took part in this criminal business, developing this substance that he was poisoned with," said Mirzayanov.
He now lives in the United States and wrote the first articles on Novichok's development in the early 1990s.
His apology comes as another scientist who worked on the program has denied that Navalny could have been poisoned with Novichok.
So far three scientists, now in their 70s, have made public statements after working on the top-secret Soviet project.