Yes they can, if reasonable cause exists.  The reasonable cause should be documented and signed under penalties of perjury.  Please review the following:
Failure to timely file the information return, absent reasonable cause, can give rise to a penalty under section 6652 of the code. Whether or not an organization qualifies for the reasonable cause exception to the penalty will be determined on a case-by-case basis taking into account all relevant facts and circumstances.
The regulations provide that a request for abatement of penalties based on reasonable cause must be made in the form of a written statement, containing a declaration by the appropriate person that the statement is made under penalties of perjury, setting forth all the facts alleged as reasonable cause. This statement should be made as an attachment to the Form 990; please disregard the Schedule O instructions that ask for this statement to be included in Schedule O.  When requesting abatement of penalties for reasonable cause, your statement should include supporting documentation and address the following items:

• The reason the penalty was charged. The daily delinquency penalty may be charged for either a late filed return, an incomplete return, or both.
• Explain what prevented the organization from complying with the law, including:
  • What prevented the organization from requesting an extension of time to file it’s return, if the organization did not request such an extension.
  • How the organization was not neglectful or careless, but exercised ordinary business care and prudence.
  • What steps have been taken to prevent the same situation from occurring in the future.
  • Documents that provide the substantiation.

  This penalty can usually be abated when handled by a professional company that knows the ins and the outs of the procedural guidelines.