The Megaupload founder, facing copyright infringement, money laundering and racketeering charges in the United States, made two $NZ25,000 donations to Mr Banks' 2010 Auckland mayoralty campaign, Campbell Live reported on Friday.
The New Zealand Herald reported that Mr Banks asked for the $NZ50,000 donation to be split so it could be recorded anonymously.
"It appears that Kim Dotcom has confirmed he donated tens of thousands of dollars to John Banks' mayoral campaign under a veil of anonymity after being asked directly by Mr Banks to do so," Labour leader David Shearer says.
Labour MP Trevor Mallard has also raised concerns about the non-declaration of a donation from casino operator SkyCity and regular donations of radio advertising to Mr Banks' campaign.
"John Key should stand John Banks down while an investigation by police is under way. He cannot continue to hold ministerial roles while such serious allegations are swirling around him.
"I urge the prime minister to confront Mr Banks about the claims and get to the bottom of what has gone on."
Mr Banks is small business and regulatory reform minister and is an associate minister for the portfolios of commerce and education.
