Nainggolan, 29, has been linked with a move to the CSL despite being contracted at Roma until 2021.
Guangzhou Evergrande Taobao are also believed to be interested in Nainggolan, but Beijing said they had never targeted the Belgium international.
"We have never approached Roma and Nainggolan has never appeared in our head coach's lists of transfer targets," the club's general manager Li Ming told Chinese reporters.
"The story of Guoan jostling with Evergrande for the signing of Nainggolan is utterly groundless.
"Beijing Guoan will not be disturbed by those [rumours] at all, let alone buy overpriced foreign players.
"We will obey all the rules set by the Chinese Football Association with regard to any foreign transfers ahead of the new season."