Rep. Lauren Boebert is flat-out denying claims made against her in a complaint submitted to Congress that she had affairs with current and former staffers and made a hush-money payment ... and is calling the accusations baseless.

A rep for Boebert tells TMZ ... "Congresswoman Lauren Boebert rejects these allegations as utterly false and there is no truth to them whatsoever. This is nothing more than a politically motivated stunt designed to manipulate the ethics process, create headlines, smear her, and generate clickbait."

They added ... "They come from an activist who has long recycled sensational claims, including numerous baseless accusations previously fact-checked as false."

The complaint -- filed by David Wheeler earlier this week with the House's Committee on Ethics -- alleges that she had sexual relationships with three current and former staffers and she paid $200,000 as hush money.

In response to her denial, Wheeler said he stood "100%" by his story and sourcing ... and claimed that the "facts are on our side."

He told TMZ that he would "continue to report on Boebert ... without fear and at personal and financial sacrifice."

He added ... "I have nothing to hide."