The Scottish Premier League night announced Hearts have "not paid a number of bonuses and appearance payments" and also face a disciplinary hearing.
It is understood some players are still awaiting bonus payments from the William Hill Scottish Cup Final win against Hibs on May 19.
The rules Hearts have been cited for relate to failure to pay players and club officials and were brought in during the summer after a series of late payments by the club last season.
Hearts acknowledged the SPL's statement, while insisting cup final bonus payments have been made.
A notice on the club's official Twitter page read: "All Scottish Cup Final bonuses have been paid."
A statement on the club website read: "Heart of Midlothian today received notification from the SPL of an embargo on the registration of players in relation to an alleged remuneration default.
"The club is consulting with its legal advisors and will make no further comment."
Hearts were initially placed under a 60-day transfer embargo on October 24 for failing to pay their players and some staff their monthly wages on time for two consecutive months. That sanction was due to end on December 23.