A fundraising email sent by the National Republican Congressional Committee (NRCC) included a photograph of Kaepernick alongside US president Donald Trump.
But the image, which showed the former sportsman kneeling down during the US national anthem at a game in November 2016, was several shades darker than the original.
A Democratic operative described the ad as “disgusting” and “offensive”.
They told Yahoo News: “House Republicans are running on racism, plain and simple.”
However some Twitter users said the image looked different because a filter had been used.
One person using Twitter handle @HarryTokus said: “They didn’t darken his skin. They just used a different filter.”
And NRCC communications director Chris Pack insisted the colour of Kaepernick’s skin had not been altered, telling Yahoo: “The photo was not darkened.”
It appears to reference Nike’s decision to pull a shoe model featuring an 18th century flag after Kaepernick objected.
The former athlete, who is endorsed by Nike, said he found the flag offensive because of its association with America’s slavery era.
The shoe featured a version of the flag believed to have been created by American upholsterer Betsy Ross in 1792, when the country’s slave trade was rapidly expanding.
In 2016, Kaepernick became the first NFL player to take a knee during the national anthem in protest of growing racial disharmony across the United States, including police shootings and instances of police brutality.
US president Donald Trump’s anger towards the protesting players prompted more to join, in turn morphing the demonstration into something of direct resistance to his administration’s handling of race issues.