TaxAct supports the filing of Form 4562 - Depreciation and Amortization with the filing of Form 990-T - Exempt Organization Business Income Tax Return.TaxAct does not support the filing of Form 4562 if you are filing Form 990 - Return of Organization Exempt from Income Tax or Form 990-EZ - Short Form Return of Organization Exempt from Income Tax.
Per the Form 990, Return of Organization Exempt From Income Tax Instructions, page 48:
Line 22. Depreciation, depletion, and amortization. If the organization records depreciation, depletion, amortization, or similar expenses, enter the total on line 22. Include any depreciation or amortization of leasehold improvements and intangible assets. An organization isn't required to use the Modified Accelerated Cost Recovery System (MACRS) to compute depreciation reported on Form 990. For an explanation of acceptable methods for computing depreciation, see Pub. 946, How to Depreciate Property. If an amount is reported on this line, the organization is required to maintain books and records to substantiate any amount reported.
Note that any link in the information above is updated each year automatically and will take you to the most recent version of the document at the time it is accessed.