Google also invested in Rubin's next venture, Playground Global, and reportedly delayed the repayment of a $14 million personal loan it gave him to buy real estate in Japan.
Aside from the allegations that led to his resignation, Rubin had previously had his bonus docked for keeping sexual bondage videos on his work computer, the report says.
When The Information first reported details last November about Google's investigation into Rubin's inappropriate relationship with a co-worker, he took a leave of absence from hardware company Essential. He has since returned to work.
Google did not immediately responded to CNBC's request for comment. A spokesperson for Rubin told CNBC:
"Mr. Rubin left Google in on his own accord in 2014 to found Playground, venture capital firm and technology incubator. He did not engage, nor has he ever been told of any misconduct at Google or anywhere else.
"Any relationship that Mr. Rubin had while at Google was consensual and did not involve any person who reported directly to him. He did have a consensual relationship that occurred in 2012. To his knowledge, at that time there were no policies in place that prohibited relationships between employees.
"Mr. Rubin is known to be transparent and forthcoming with his feedback and in rare situations doesn't mince words when debating the work of troubled efforts. In that context commentary such as "well that won't work" or "that's dumb, how about this" is in character for Mr. Rubin during these product reviews. At no time did Mr. Rubin ever direct these comments towards an individual or a group, and at no time did Mr. Rubin call anyone incompetent."
Read the full New York Times report here.