The ruling came after Alamo's former followers testified at a hearing that they were often beaten at his instructions and one said Alamo practiced polygamy with several females, including a 9-year-old girl.
U.S. Magistrate Judge Barry Bryant noted that Alamo is charged with a violent crime and said he also considered that Alamo fled a California child-abuse charge in 1989 and was arrested two years later in Tampa, Fla., living under an assumed name. Alamo has access to various vehicles, he said.
Witnesses said Alamo controls businesses and ministry locations in several states. They said none of the properties are Alamo's name, which Bryant also considered as a point against letting Alamo free.
"There is serious risk (Alamo) will flee or fail to appear," Bryant said.
Alamo, 74, said nothing after the ruling. His trial is scheduled for Nov. 19.
He was arrested in Flagstaff, Ariz., five days after a Sept. 20 police raid on the Tony Alamo Christian Ministries compound in the southwest Arkansas town of Fouke. Six girls were taken into state custody for their protection.
During Wednesday's hearing, Arkansas state troopers searched the compound anew, State Police spokesman Bill Sadler confirmed, not elaborating. Fouke Mayor Terry Purvis said residents told him the investigators did not stay long.
One witness called to the stand by prosecutors Wednesday, Jael Sprinkle, 32, testified that she was taken as Alamo's wife at age 17 and was considered his wife for two years. She said that Alamo had five other wives at the time and that she knew of him taking a 9-year-old girl as one.
Alamo is an advocate of allowing girls to marry when they reach puberty but has denied such unions took place within his organization.
Sprinkle said she, her parents and others were beaten. She said a 12-year-old boy was paddled to the point of bleeding through his clothes and could walk only with assistance.
Sprinkle also described Alamo's control over people in his organization, saying he even had to approve inconsequential expenses such as toilet paper and toothpaste.
Spencer Ondirsek, 18, testified that he left the compound last year after spending seven years there.
Ondirsek said he was beaten by a man working under Alamo's direction. He said he was hit about 15 times on the face and smacked about 30 times with a three-foot paddle in three separate instances while being disciplined for minor misbehavior, such as playing with a spray bottle.
The first beating happened when he was 12 or 13, Ondirsek testified.
Defense lawyers called Ronald and Joan Decker, a couple that has belonged to Alamo's church. They said they would move from Fort Smith to Texarkana to watch over Alamo if he was granted release.
Ronald Decker said he drives a truck for Advantage Food, which he described as a partnership, but he couldn't come up with a figure when federal prosecutor Kyra Jenner asked him how much he earned. He later said Alamo paid for all the couple's living expenses.
"Pastor Alamo controls the church," Ronald Decker said.
Ronald Decker initially denied seeing any beatings. But when asked by Jenner whether he was aware Alamo orders paddlings, Decker paused before saying yes.
The federal charging document accuses Alamo of taking a 13-year-old girl across state lines for sex in 2004 and of aiding and abetting her transport across state lines for sex in 2005.
Alamo, who is listed in court documents by his real name of Bernie Lazar Hoffman, has pleaded not guilty to the two charges, each of which carries a sentence of 10 years to life in prison and a fine of up to $250,000.