The Sabarimala shrine was in controversy after the Supreme Court in 2018 lifted the bar on entry of women aged 10-50 entry.
Khan clarified that he had no differences with the government and the reports to the contrary were misleading.
The Governor has given the nod for the session, days after the CPI(M) led LDF government sent a fresh proposal to convene the assembly after he had turned down an earlier recommendation.
The meeting came even as the government and Left parties continued their attack on the Governor over his earlier decision refusing permission for a special session on December 23.
The policy address is to be delivered by the Governor as the Kerala Assembly convenes for the Budget session on January 8.
Cabinet that met today decided to once again send a recommendation to the Governor seeking a special session on December 31. This time, sources said, the Governor will have no choice but to accede to the request.
Top sources said the Governor had rejected the State Government's recommendation saying there was no urgency for convening a special session.
The Congress chief's criticism of the Governor came during a protest that was held in front of the secretariat here against the amendment.
Arif Mohammed Khan was admitted to the government medical college hospital on November 9 after he tested positive for COVID-19 on his return from New Delhi.
Khan, 68, was diagnosed with the infection on his return from New Delhi.