The Wall Street Journal reports more than $12 billion in revenue reported by the drug giant was never collected by the company's pharmacy-benefits unit.
The Journal says the payments amounted to almost 10 percent of Merck's overall reported revenue the past three years.
One financial advisor says while the incident is still being looked at, this is a wake-up call to employees and investors.
"Having your money diversified, having it not all in your company, especially in this day and age continues to be a real important thing. Especially in this day and age where accounting irregularities and those sorts of things are happening pretty regularly," explains American Express Financial Advisor James Hiter.
Representative for Merck say these are generally accepted accounting practices and the practice has not impact on the company's bottom line.