The warning comes from specialist insurer Ecclesiastical.
In April, thieves broke into St Mary's Church in Hainton and took a bishop's chair and two carved angles from the alter area.
The Reverend Annabel Barber said the items had been in the church for hundreds of years so it was “very sad”.
Ecclesiastical advised churches to review their security arrangements, but said clergy should still keep buildings open during the day.
Ms Barber said it was important St Mary's Church remained open.
She said: “There are people who want to use the church but who don't want to come to Sunday services, but they will go into a church if they're passing or if something is on their mind, and they want somewhere to sit peacefully for a few minutes.
"If we lock the churches, then we are preventing people from being able to do that."
Change in attitude
The insurance company said a number of churches had been targeted in the first half of 2024, including one in Birmingham where a thief was caught on CCTV making off with a Victorian brass eagle lectern.
The firm said silverware and other valuables should be kept in safes and that churches should be locked at night. They also advised installing intruder alarms and CCTV.
Ms Barber said she thought that there had been a change in attitude towards churches.
She said: “There is, in a sense, a loss … of a consideration of the holy, and the church is no longer viewed as being a particular type of special public building.”
Ms Barber said churches in the Lincoln diocese were under a continual threat from thefts, especially those located near to main roads.