Kwame Andoh Kyei suffered serious injuries after he was attacked while running the line during a match between Gold Stars and Naa Joe United in Bordie on March 2.
He died on Friday as a result of the injuries.
"Doctors are yet to fully establish the cause of his death," said the GFA statement.
"He was regarded as one of the association's most promising up and coming referees and was highly respected by his peers.
"A meeting of key stakeholders will be called by the GFA after receiving the report to examine the immediate action to be taken while the police continue with their investigations," the statement from GFA president Kwesi Nyantakyi added.
Local media reports said Kyei had not been hospitalised after the beating by supporters of Gold Stars.
"My brother had told us he was going to officiate a match and when he returned he told us of an incident that occurred in the match," his brother Kweku Andoh Kyei told Accra-based radio station Asempa FM.
"He was even joking about how one guy gave him a slap while others manhandled him," he added. "But on Friday I was called and told that my brother was vomiting blood and had fainted."
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