I attend a church that is under a 501c-3 non profit organization on our last meeting the funds in the operating account for bills and to pay salary is low not enough to cover expense, so the pastor and staff had to take a 25% cut in their pay. The church has money in a cd and a money market account but they said they will not touch that money and the pastor and staff might not get paid next month if there is no money in the operating account, I need to know can a non profit hold mony in any kind account or cd etc and not use that money?

There are no rules that prevent the church (or any organization for that matter) from cutting pay of its employees, absent a contract that guarantees pay (such as a union contract), even though the organization has some cash in the bank. So yes - the church can continue to hold a CD or other financial assets even while it cuts the pay of its employees.