The Nigeria Referees Association (NRA) ordered that all the referees slated to officiate in the Premier League should withdraw from matches "until sanity is restored" in the national game.
The directive, contained in a circular signed by NRA secretary-general Moroof Oyekunle Oluwa, also applied to the second-tier National League, Nigeria Federation Cup and the women's leagues.
The premier and national league are both in their 25th week of action. Defending champions Kano Pillars currently top the log table with 43 points.
Nigeria's football association has been in crisis since last month, when world governing body Fifa suspended the country from all international competitions over what it said was "government interference" in the running of the game. The ban was later lifted.
Nigeria Football Federation (NFF) president Aminu Maigari was dismissed on charges of embezzlement, then reinstated because of procedural irregularities before being held by the country's secret police for an unspecified reason.
This week, a new president was appointed in Maigari's place in defiance of a Fifa order only to set a date for fresh elections of the association's high command, raising the possibility of fresh sanctions.
To top it all, the NFF headquarters in Abuja were gutted by fire and national team coach Stephen Keshi has been locked in a wrangle over a new contract, just weeks before the start of qualification for next year's Africa Cup of Nations. Nigeria are defending champions.
Already, the country's Coaches Association has distanced itself from the NFF, while soccer writers have called on President Goodluck Jonathan to intervene.