Even worse, seven insurance companies did not file until after the IRS had come up with its final fee assessments for the companies that had filed.

That means that insurers that made the deadline likely ended up paying more than their intended share, since the IRS calculates the fee based on each insurer's market share of overall premiums. The $8 billion revenue goal was set beforehand, with each insurer that filed being charged a certain fee to get to that figure.

But the IRS thus did not take into account the billions of dollars of premiums from insurers that filed late. 

The tardy filers could face up to $4.9 million in late fees. But currently there is no process for the IRS to correct the fees it has already assigned to companies that filed on time. 

"The lack of a reconciliation process allows covered entities that do not timely file required Forms 8963 to be exempt from paying their portion of the annual fee," explained J. Russell George, the Treasury inspector general for tax administration. "This in turn results in covered entities that comply with the timely filing requirement paying more than their fair share."

Many insurers remain unaware of key aspects of the fee requirement.

Insurers that generate more than $25 million of premiums are subject to the fee. 178 insurers reported receiving less than that amount and were thus not required to pay the fee. 

This is not the first time the IRS has come under fire for failing to administer key provisions of the PPACA. Another recent report said the tax agency has failed to deliver subsidies to many who have signed up for plans on the PPACA insurance exchanges.