He began to sexually assault her in the fall of 2014, she told police.
The teenager told police Malone gave her alcohol twice after she turned 18. Once when she became highly intoxicated, Malone molested her, she said.
In November 2015, church leaders learned of the girl's pregnancy and of Malone's alleged inappropriate relationship in another state with a female whose age Bateman would not disclose.
The church leaders confronted Malone, he admitted he impregnated the teenager, and he resigned in mid-November, Bateman said.
Early last month, the young woman moved out of Malone's house and temporarily moved in with a church member. She has moved out of state to be with family, Bateman said.
Police said Malone met the girl when she was about 12 and a member of a church in Mesa, Ariz., where Malone was serving as a pastor.
Police said several years later, in June 2014, Malone contacted the girl, who was 17. He invited her to stay with him and his family in Minnesota, where he had become a pastor.
The girl said Malone then began trying to have "inappropriate contact" with her, police said.
Bateman said church leaders told the Calvary congregation about the allegations on Sunday.
"Our church's goal in difficult moments like this is to protect the innocents, first of all," Bateman said in an interview Monday. "And, number two, we strive to bring about repentance and restoration of the offender."
Bateman said Malone had passed background checks performed on Calvary employees.
Police are asking anyone with information on Malone's location to call the West Whiteland Police Department at 610-363-0200 or 610-692-5100. Callers can leave anonymous messages on the tip line at 610-594-9057.