The charges against the 37-year-old man and his 35-year-old wife were referred to a grand jury on Tuesday in Tazewell, which is in rural Claiborne County near the Kentucky border.
The man is charged with aggravated child abuse and two counts of rape. His wife, who prosecutors say knew about the use of dog collars but not the alleged sexual assaults, is charged with aggravated child abuse and failure to report child abuse.
Prosecutors said more charges could be handed down when the grand jury convenes Dec. 3.
The husband and wife were identified in court, but The Associated Press is withholding their names to avoid identifying their daughters. The AP generally does not identify possible victims of sex abuse.
The wife's attorney, Buddy Baird, said his client will be vindicated when the facts come out. He refused to elaborate. The father's attorney, Dale Potter, did not return a call for comment.
The man used remote-controlled shock collars to force his two eldest daughters - now ages 18 and 19 - to obey him, said Capt. Sam Nelson, the lead investigator at the Claiborne County Sheriff's Office.
The two girls are from their father's previous marriage. The couple has three other children, a girl and two boys, but none of the abuse allegations relate to those children, prosecutors said.
The 18-year-old girl said her father raped her and her sister for a period of about five years, from when they were in their early teens, said prosecutor Amanda Sammons. The girl said he raped her in the family's mobile home and in the woods, Nelson said.
The girl said her father put a shotgun to her head "and said that if she ever told anyone, he would kill himself, her and anyone who tried to remove her from the home," according to an affidavit filed by Nelson.
She had been too scared before to tell authorities, but was now "scared for her younger sister, who was 11. She was afraid that her father was going to do the same thing to her," Nelson said.
The girl, then 17, told an official at her high school about the abuse on Sept. 10, and the couple was arrested the following day, Nelson said. The man was being held on $1 million ( EUR 680,000) bond. His wife has been released on $100,000 ( EUR 68,460) bond.
The four youngest children, including the 18-year-old, are in foster care. Authorities don't know the 19-year-old girl's whereabouts.