The SPL announced Hearts have "not paid a number of bonuses and appearance payments." The club face a disciplinary hearing, with a full range of sanctions at the league governing body's disposal.
Hearts said they were taking legal advice and manager John McGlynn revealed: "We're going to challenge it.
"It's difficult to talk about it because we're going through lawyers."
Hearts insisted that bonuses from the Scottish Cup final win over Hibernian on May 19 had been paid. If so the payments were probably in this month's pay packet on December 16 - six months late.
Payments of other bonuses due this season are understood to be in arrears, amounting to a six-figure sum.
Hearts argue there is no set date by which bonus payments must be made.
The rules that Hearts have been cited for relate to a failure to pay staff and were brought in after a series of late payments by the club last season.