The Alabama warrants charged the trio with arson in Bibb County, where five of the nine blazes occurred early last month, and officials said charges were possible in the western Alabama counties where four more small Baptist churches were torched.
"Even if they make (the federal) bond they will not be going home," U.S. Attorney Alice Martin said.
The three were arrested March 8 on federal charges of conspiracy and setting fire to one of the churches. Evidence indicates the fires began as a prank that went out of control on a night of drinking and hunting. Defense attorneys have said the fires were not crimes of hate.
In a brief order, U.S. Magistrate Judge Robert R. Armstrong Jr. had said the three suspects could be released on bonds of $50,000 each, provided they stay away from alcohol, cars and home computers. They could live with their parents in what amounted to house arrest with electronic monitoring while awaiting federal trial.
But with the filing of state charges, the three would instead be transferred immediately to the Bibb County Jail, south of Birmingham, if released on federal bond.
A lawyer for suspect Matthew Lee Cloyd, 20, said his client would not seek federal bond, allowing him to remain jailed in Shelby County, near his parents' home. The lawyer, Tommy Spina, said it was too early to discuss the possibility of a plea.
Attorneys for the other two, Benjamin N. Moseley and Russell L. DeBusk Jr., both 19, did not immediately return calls seeking comment.
In the federal order, Armstrong had noted that none of the three has a criminal record, and all come from "normal, stable, caring, working-parent homes," but also that all are under 21 and "drink alcoholic beverages in amounts that would be excessive for adults."
The federal judge had rejected prosecutors' plea that the three remain jailed until trial.
According to court documents, Cloyd told a witness that he and Moseley "had done something stupid" and that they set fire to a church "as a joke."
The men torched five Bibb County churches on Feb. 3, according to the federal agent's sworn statement. According to the statement, Moseley told investigators he and Cloyd set the other fires four days later as a diversion.
Meanwhile, a "service of grief and hope" over the fires and arrests was planned at Birmingham-Southern College, where Moseley and DeBusk are students. Both men have been suspended.