Plateau United Feeders crushed Akurba 79-0 while Police Machine demolished Babayaro 67-0 in third division promotion play-offs.
Both winning teams had been looking for a superior goal difference to advance.
"It is unacceptable, this is a scandal of huge proportions," Nigerian Football Federation vice president Mike Umeh told reporters on Tuesday.
"The four teams involved are suspended immediately and indefinitely pending further sanctions. We will investigate this matter thoroughly and get to the bottom of it."
Feeders scored 72 goals in the second half while Police Machine netted 61 after the break.
Going into the last round of the play-offs, Police Machine and Feeders were level on points.
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