Rampage by 19-year-old in Omaha leaves eight dead and another five wounded.
One of the injured at the church later died.
Lieutenant Fletcher Howard said police were not sure if a second gunman was still at large but had cordoned off the church and locked down several buildings.
In the first incident hours earlier in the town Arvada, police said a man opened fire and killed two employees of the Youth with a Mission (YWAM) organisation.
Two other men, aged 22 and 23, were being treated for gunshot wounds, a police statement said.
YWAM said a young man who had gone to the YWAM dormitory asking for a place to stay but was told he could not be accommodated there, pulled out a handgun and opened fire shortly after midnight.
The incident in Nebraska revived the debate about gun crime in the US, which the authorities say is home to more than 200 million privately owned firearms for a population of just over 300 million.