It quoted GHALCA chairman Emmanuel Adotey on its website as saying the confiscation by police of FA computer equipment and files meant that various decisions affecting the running of the leagues could no longer be administered.
"The confiscation of equipments and files has necessitated their pulling out since various decisions including disciplinary cannot be confirmed and communicated to all affected clubs and players," it quoted Adotey as saying.
Earlier, football's governing body FIFA said it was monitoring events in Ghana after plain-clothed officers from the country's Economic and Organised Crime Unit (EOCU) removed nine computers and took the mobile phones of some staff in Tuesday's raid.
Ghana reached this year's World Cup quarter-finals, losing a penalty shootout to Uruguay, after being denied what would have been a winning goal at the end of extra-time when opposing forward Luis Suarez handled the ball on the line.
Ghana's World Cup success means it may now experience the same problems as other African football nations such as Cameroon or Nigeria, with the arrival of private sponsors creating friction with the government.
