There are a couple of options at your disposal:
First time abatement can provide penalty relief if the taxpayer has not previously been required to file a return
or has no prior penalties (except the estimated tax
penalty) for the preceding three years with respect to the same IRS
Master File module (IRM §220.127.116.11.6.1). With respect to a Form 5472 late-filing penalty, the IRM provides for an FTA if an FTA was applied to the taxpayer's related Form 1120 late-filing penalty or no penalty was assessed on the related Form 1120 (IRM §18.104.22.168.2).
Secs. 6038 and 6038A each provide a reasonable-cause basis for penalty relief (Regs. Secs. 1.6038-2(k) (3), 1.6038-3(k)(4), and 1.6038A-4(b)). A taxpayer may qualify for penalty relief based on reasonable cause if the taxpayer exercised ordinary business care and prudence in determining its tax obligations but was nevertheless unable to timely file the return to which the Form was attached.
As of July 1, 2014, taxpayers that have failed to file a Form 5472 may file it under the IRS's Delinquent International Information Return Submission Procedures. The procedures allow taxpayers to avoid penalties under Secs. 6038 and 6038 A if the taxpayer timely filed its original income
tax return but omitted the required international information forms.
The procedures are available for taxpayers that (1) have not filed one or more required international information returns, (2) have reasonable cause for not timely filing the information returns, (3) are not under a civil examination or a criminal investigation by the IRS, and (4) have not already been contacted by the IRS about the delinquent information returns. Taxpayers who have unreported income or unpaid tax are not precluded from filing delinquent international information returns.
Taxpayers that meet the requirements should file the delinquent information returns with an amended income tax return and attach a statement of all facts establishing reasonable cause for the failure to timely file the international information returns. As part of that statement, taxpayers must certify that any entity for which the information returns are being filed was not engaged in tax evasion. The reasonable-cause statement must be signed under penalties of perjury.
If a taxpayer does not attach a reasonable-cause statement to each delinquent information return filed, penalties may be assessed in accordance with existing procedures. The IRS also may impose penalties if it does not accept the taxpayer's explanation of reasonable cause.
If a taxpayer meets the requirements for and follows these procedures, the IRS presumably will not automatically assess penalties under Secs. 6038 and 6038A for the late filing of the form.