"The amount of tax being paid by these businesses is $100 billion less than reported in their accounts," he said.

Speaking to CNBC via telephone on Monday, Paul Monaghan, CEO of Fair Tax Mark, said there was an enormous difference between what companies accounted for and what they actually handed over in taxes.

Researchers said the bulk of the shortfall "almost certainly arose outside the United States," with foreign tax charges amounting to just 8.4% of the profit the companies made overseas during the decade.

The report noted that scrutiny of big corporations' tax payments often focused solely on tax provisions, which was not always the final amount received by governments. It also claimed that profits continued to be "shifted to tax havens, especially Bermuda, Ireland, Luxembourg and the Netherlands."

It looked at tax provisions — the amount companies set aside in their financial reports to pay taxes — and compared those to the amounts that were actually handed over to the government, referred to as cash taxes. Over the decade, the gap between the Silicon Six's provisions and the taxes they actually paid reached $100.2 billion, researchers found.

The research, published Monday, analyzed their 10-K filings, which are financial forms submitted by businesses to the U.S. government.

Fair Tax Mark, a British organization that certifies businesses for good tax conduct, assessed global tax payments from Facebook, Apple, Amazon, Netflix, Google and Microsoft between 2010 and 2019. The companies are sometimes collectively referred to as the "Silicon Six."

Six of Silicon Valley's biggest companies had a combined "tax gap" of more than $100 billion this decade, according to a new analysis.

Amazon was named the worst offender of the six firms, with the report claiming the e-commerce giant had paid $3.4 billion in income taxes since 2010. Fair Tax Mark noted that cash tax paid by the organization amounted to 12.7% of its profit over the decade, despite corporate tax in the U.S. being set at 35% for seven of the years included in the analysis period. President Donald Trump cut corporation tax rates from 35% to 21% in 2017.

"The company is growing its market domination across the globe on the back of revenues that are largely untaxed and can unfairly undercut local businesses that take a more responsible approach," the report said.

Amazon finished 2018 with $232.9 billion in annual revenue and the company has a market capitalization of around $892 billion.

In an emailed statement, a spokesperson for Amazon told CNBC that the suggestions made in Fair Tax Mark's report were wrong.

"Amazon represents about 1% of global retail, with larger competitors everywhere we operate, and had a 24% effective tax rate on profits from 2010-2018," the company said.

"Amazon is primarily a retailer where profit margins are low, so comparisons to technology companies with operating profit margins of closer to 50% is not rational. Governments write the tax laws and Amazon is doing the very thing they encourage companies to do — paying all taxes due while also investing many billions in creating jobs and infrastructure. Coupled with low margins, this investment will naturally result in a lower cash tax rate."

The spokesperson added that Amazon had invested 55 billion euros ($60 billion) across Europe since 2010 and £18 billion in the U.K., and had paid £793 million in taxes to the U.K. alone last year.

Facebook had the second biggest tax gap, according to the report. The cash tax it paid represented just 10.2% of the profit the company made over the decade, researchers said — the lowest proportion paid by any of the Silicon Six. Its foreign tax charge was also the lowest of the six, Fair Tax Mark noted, at 5% of foreign profits.

A spokesperson for Facebook told CNBC in an emailed statement that the company takes its tax obligations seriously, paying what it owes in every market the firm operates.

"In 2018 we paid $3.8 billion in corporation tax globally and our effective tax rate over the last five years is more than 20%," they said. "Under current rules we pay the vast majority of the tax we owe in the U.S. as that is where the bulk of our functions, assets and risks are located. Ultimately these are decisions for governments and we support the OECD process which is looking at new international tax rules for the digital economy."

Google was ranked third, with the report claiming its taxes amounted to 15.8% of profits, while its foreign tax charge was 7.1% for the decade.

A Google spokesperson told CNBC in an email that Fair Tax Mark's interpretation of how the company paid taxes "ignores the reality of today's complicated international tax system and distorts the facts documented in our regulatory filings."

"Like other multinational companies, we pay the vast majority — more than 80% — of our corporate income tax in our home country," they said. "As we have said before, we strongly support the OECD's work to end the current uncertainty and develop new tax principles."

Netflix, ranked fourth, handed 15.8% of its profit over, while Apple, in fifth, had a tax rate of 17.1% over the decade, according to the study.

"As the largest taxpayer in the world, we know the important role tax payments play in society," a spokesperson for Apple told CNBC in an email. "We pay all that we owe according to tax laws and local customs wherever we operate, and since 2008 Apple's corporate taxes alone have totaled over $100 billion."

Netflix declined to comment on the study's findings.

Microsoft, which paid the highest rate of tax, had a cash tax rate of 16.8%, the research showed.

"Microsoft is fully compliant with all local laws and regulations in every country in which we operate," a spokesperson told CNBC via email. "We serve customers in countries all over the world and our tax structure reflects that global footprint."