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.
The decision means clubs will not be involved in the Glo Premier League, Division One, Two and Three football leagues until further notice.
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.
FIFA does not tolerate government interference in football and in October it briefly suspended Nigeria following court action against directors of the federation.
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.
The Ghana Football Association (GFA) has not given reasons for the raid but noted authorities had two months ago requested information on all sponsorship contracts signed by the GFA.
It added that it had sought extra time to gather the documents but had not received a response.
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.
