The suspect offered no resistance when about 20 federal agents entered his home, said Mark James, special agent in charge of the Kansas City office of the Alcohol, Tobacco and Firearms.
Authorities would not say who lived in the home, but relatives and neighbors identified the resident as 43-year-old James "Jamie" Schwartz.
The standoff began Thursday afternoon at the home about eight miles north of Salem on Missouri 68 when agents tried to serve a federal search warrant and an occupant refused to come out.
A woman left the home Thursday shortly after officers arrived. James would not say where she was or if she had been arrested. No children were in the home when officers arrived.
James said he could not discuss what prompted the search warrant because it had been sealed by a judge. He would say only that agents "found what we were looking for."
Denton County Sheriff Bob Wofford said his department had previous contact with the suspect but he declined to elaborate.
"We knew there was activity here," Wofford said.
The suspect is expected to be arraigned before a federal magistrate in St. Louis, possibly as early as Monday, James said.
A team of 12 negotiators had been unsuccessful in contacting the man throughout the siege, despite using bullhorns, a telephone and robots equipped with audio and visual capabilities.
James said officers decided to enter the home in part because they were concerned about the man's condition.
"The individual would not answer us or respond to us," James said.
About 100 officers, including some from U.S. Customs, surrounded the home throughout the standoff.
Portions of Missouri 68 were closed and two homes located nearby were evacuated. James said the inconvenience caused by the standoff also was a factor in deciding to enter the home.
Mike and Mary Mrozowicz, who live in a nearby home that was not evacuated, said the ranch-style house also has a mobile home on the property.
The Mrozowiczes said they've seen men wearing camouflage clothing and helmets hiding in the nearby woods with guns.
They said they've seen agents coming and going over the last couple of days, but the agents weren't giving area residents any clues what they were doing there.
The warrant was ordered out of the eastern district of Missouri. Jan Diltz, spokeswoman for the U.S. Attorney's Office in St. Louis, said she could not discuss the warrant.