The indictment comes as Nocks was awaiting trial in the state's 2nd District Court in May on negligent homicide charges. That case will soon be dismissed in lieu of federal prosecution.
Nocks and Bugman Pest and Lawn are accused of causing the deaths of Rebecca Toone, 4, and her 15-month-old sister, Rachel, in February 2010. They died a few days after Nocks used a pesticide called Fumitoxin to get rid of rodents around the Toone family's Layton home. Investigators allege that Nocks used too much Fumitoxin and placed it too close to the home.
Coming nearly a year after Nocks applied Fumitoxin at the Toones' home, the indictment also covers its use at residences in Centerville and North Salt Lake, where it was applied inconsistently with its labeling in September and May of 2009, U.S. Attorney Carlie Christensen said in a statement.
"We believe evidence shows there has been more than a single violation by the company and its employee, Mr. Nocks," Christensen said.
"Strict regulations are in place for dealing with registered pesticides because of the potential for serious harm if they are applied incorrectly. When homeowners hire pesticide service companies, they have a right to expect that the company and its representatives will follow those rules and regulations," she said.
"When that trust is broken, we have the type of tragic outcome that led to today's indictment."
In a statement Wednesday night, the Toone family voiced its support for the government's case.
"We reaffirm our intent to cooperate with government officials who pursue justice for the deaths of our daughters, Rebecca and Rachel," Nathan and Brenda Toone wrote in the statement.
Nocks and Bugman owner Ray Wilson did not respond to calls seeking comment.
Assistant Layton City Attorney Steve Garside said in a statement that the choice to transfer the case from state to federal court will "facilitate a more efficient use of resources, precluding a duplication of processes, while achieving the same objectives."
Nocks whose state license was stripped last summer previously told The Salt Lake Tribune that he does not believe his actions caused the girls' deaths.
Nocks told The Tribune said he had lined up three expert witnesses for his state case, including an expert on carbon monoxide who was going to testify that high carbon monoxide levels in the Toones' home could have caused the girls' deaths.
Since the Layton poisonings, the U.S. Environmental Protection Agency has further tightened the use of Fumitoxin. It is no longer permitted for use in residential areas.
Nocks and his former company's case has been assigned to U.S. District Court Judge Dee Benson, but an initial appearance date had not been set as of late Wednesday.