District Attorney Lance Marshall said there was insufficient evidence to back up the initial claim that the woman was raped or assaulted on average 14 times a month for 13 months, which he said was "hard to believe."
"Was there enough covered to pursue to a jury 1,100 counts? I don't think so," he said.
Chamberlin also agreed to stand trial on one count each of terroristic threats, reckless endangerment and theft, Marshall said.
Chamberlin, who was unemployed and lived with his parents, was in jail in an unrelated case when police in December filed 1,100 counts against him in connection with the alleged sexual assaults, including the 183 counts of rape.
State police had said in a complaint that Chamberlin assaulted the woman regularly starting in August 2006 after sneaking into her house once her husband had left for work. They said she was too terrified of Chamberlin to report the alleged attacks to either her husband or police.
Most of the alleged assaults took place at her home in the rural borough of Centre Hall, near State College, police said.
Marshall said police conducted a thorough investigation and should not be criticized, adding that "there were a number of people that corroborated certain acts."
Wearing red prison garb, Chamberlin did not speak as he briefly walked through the courtroom Wednesday afternoon.
"We're just looking forward to a resolution of this and another case," defense attorney Charles Kroboth Jr. said outside the courthouse, declining further comment.
Chamberlin was jailed Oct. 1 in an unrelated investigation after police said he set fire to a mobile home in Centre Hall on two occasions after arguing with the trailer's occupants. He is awaiting trial on a charge of attempted murder and multiple counts of arson.
Police found him at the woman's nearby home while investigating the second fire. Fearing for her safety, the woman did not come forward and talk to police until after Chamberlin was charged in the arson case, authorities said.
Chamberlin was sentenced Tuesday to 1 to 2 years in prison for statutory sexual assault in a third, unrelated case.
