Cummins was wanted on allegations of aggravated kidnapping and sexual contact with a minor. When they reached out to the Siskiyou County Sheriff's Office, they were informed the same person already called them.
Police say the teacher kidnapped the girl from Columbia, Tennessee, on March 13.
Authorities had earlier said the arrest happened at a commune but later clarified that it occurred in a very remote area and that they were still collecting evidence.
A lawyer for Thomas' family says they are elated the girl has been located safely.
Investigators say the two were hiding in a remote cabin in northern California.More news: Bill introduced to ban removal of passengers
Tad Cummins, 50, who was found Thursday with the girl in a cabin in a remote corner of Northern California, was taken from a jail cell in Yreka, about 60 miles (100 km) south of the OR border, by federal agents shortly before he was due to make an appearance in a California state court.
Siskiyuou County Sheriff Jon Lopey told Inside Edition that the teen is on an emotional rollercoaster. "It may be a long road, but at least we've got her back now", he said.
Court papers filed recently in the girl's disappearance said she was afraid of the teacher and thought she would face repercussions at school if she resisted him.
TBI, FBI and Maury County authorities flew to California Thursday afternoon, and planned to bring Thomas home on a TBI plane Friday.
"It only takes one tip", said Mark Gwyn, Director, Tennessee Bureau of Investigation, "and this is yet another example of the value of the public helping us to rescue a kidnapping victim".
The girl was apparently healthy and unharmed, and authorities said their main concern was her emotional and mental state.More news: Spurs in shock at coach's tragic death
He could get a minimum of 10 years in the slammer on the federal charges alone. Cummins came out of the cabin willingly and was arrested. The search for the pair spawned Amber alerts in Tennessee and Alabama, a sighting in Oklahoma City and more than 1,500 tips before they were found this week in Siskiyou County, which borders Oregon.
He had just been suspended from teaching and police were zeroing in on him, questioning his relationship with the girl. But instead, authorities say he picked the student up in Columbia, Tennessee, setting off a six-week police manhunt. An AMBER Alert was issued for her the next day.
Her accused kidnapper Tad Cummins is being held in federal custody in Sacramento, California.
Fact: It's unclear exactly what kind of sexual contact took place between the pair, but Cummins has not been charged with rape.
Cummins' estranged wife, Jill, released a statement saying she is "glad this chapter of the ordeal is over".More news: Snap poll expected to strengthen Theresa May
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