Police detained the 45-year-old man Friday in the eastern city of Siedlce after his wife and daughter came forward with the allegations, national police spokesman Mariusz Sokolowski said on private TVN24 television.
The accusations recalled the case of Josef Fritzl, who police say has confessed to having kept his daughter captive for 24 years in a cellar below his home in Austria, sexually abusing her and fathering seven children with her.
"To some extent, this could be a similar situation to that in Austria," Sokolowski said.
Polish police will conduct tests on the boys to determine if the man is the father and are investigating whether to bring formal charges of forcible incest, regional police spokesman Jacek Dobrzynski told The Associated Press.
The man will be held for three months during the investigation, after which the court can extend his detention.
The man's daughter, now 21, told police that the man had raped her repeatedly while keeping her captive for six years in a room with no door handles, Sokolowski said. His wife corroborated the story, Sokolowski said.
Sokolowski said the girl was let out of the room on occasion, including for the births of her two sons in hospitals.
The first boy was born in February 2005 in the southwestern city of Wroclaw, and the second in January 2007 in the northeastern area of Siemiatycze, where the family had moved, Sokolowski said.
Both times, the daughter told police, she was accompanied by her father, who then forced her to give the children up for adoption, the spokesman said.
Police are searching for the boys through the hospitals that placed them for adoption, and would conduct paternity tests on both, Dobrzynski said.
Police declined to provide further information and did not offer an explanation of why the mother and daughter did not come forward earlier.
"There are very many questions in the case, and talking to the woman is very difficult because she is very emotional about what has happened to her," Sokolowski said.