Are there tax-exempt organizations that cannot file Forms 990 or 990-EZ electronically?
Most tax-exempt organizations are able to file electronically. For tax year 2006 and later, exempt organizations can electronically file amended and final returns.
Exceptions to electronic filing for exempt organizations include the following returns:
Name change returns
Short-year/short period returns, except for short period final returns
Returns from organizations not recognized as exempt: e.g., application pending, etc.
Returns older than the two prior years. MeF accepts the current tax year plus two prior tax years. For example, an exempt organization can e-file its 2012 return, plus the 2013 and 2014 returns.
For additional information on exceptions to e-filing, see Publication 4163.