The sub-group will meet again on September 4 to iron out the differences and finalise its report, which will be submitted to the Prime Minister.
"The chief minister's sub-group on CSS will meet on September 4. Some members of the panel refused to sign the final report and did not agree on certain recommendations," a source said.
The panel has recommended increasing the share of flexi funds to 25 per cent from the current 10 per cent.
Then the panel's convener Madhya Pradesh Chief Minister Shivraj Singh Chouhan had said: "There is a broad consensus on reducing the number of CSS and having two types of schemes. Some more suggestions have come... After seeking all chief ministers' consent on the draft, the final recommendations will be submitted to the Prime Minister."
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The sub-group was constituted by the Prime Minister in March this year in pursuance of a decision taken in the first meeting of the governing council of NITI Aayog a month earlier.
Meanwhile, the Centre has decided to raise states' share in taxes to 42 per cent from 32 per cent, which means larger devolution.
According to Budget estimates, the devolution to the states would be Rs 5.24 lakh crore in 2015-16 as against Rs 3.38 lakh crore, as per revised estimates of 2014-15.
Besides, Rs 3.04 lakh crore would be transferred by way of grants and Plan transfers. Therefore, the total transfer to states will be about 62 per cent of the total tax receipts this fiscal.