"Between 2013 and 2016 mining giant Glencore paid over $75 million to Dan Gertler, a controversial businessman accused of bribing senior officials in Democratic Republic of Congo to advance his mining interests," Global Witness said in a statement.
"These payments were due to be (made) to Congo's state mining company Gecamines under the terms of the original contract it had with Glencore," said the environmental and corruption watchdog.
Instead, however, they were made to Gertler, whom Global Witness described as "a friend of the Congolese President" and "a known corruption risk".
But in a statement on Friday, Glencore said the payments had been made "in accordance with a payment instruction from Gecamines".
The group also said it had complied with all its disclosure obligations.
In a separate statement, Gertler's Fleurette Group flatly denied any wrongdoing, and instead accused Global Witness of using "amateur, immature financial calculations that do not follow even the basic valuation techniques used by all professionals in this field".
It also said Global Witness's report "either misunderstands or ignores the basis economics of this deal (the sale of royalties) which produced significant value for Gecamines and a loss to Fleurette".
In November, Global Witness said the vast, mineral-rich DR Congo's state mining company had signed up to $880 million of royalties over to an offshore company owned by Gertler -- "more than Congo's annual health spending".
"Typically royalties like this are for the benefit of the population. This is especially vital in Congo, which ranks near the bottom of the UN Human Development Index and has one of the lowest rates of GDP (gross domestic product) per capita in the world."
Joseph Kabila took power following his father's assassination in 2001. He has faced unprecedented pressure to stand down in recent months after his term expired in December.
As political tensions soared, he struck a power-sharing deal with the opposition on New Year's Eve that provides for elections late this year.