In a Facebook post, he said Kerala hasstrong objections to many proposals of the Centre on GST and sought to know if it would try fora consensus and consider different opinions.
He also took exception to the voting procedure for the selection of Vice-chairman of the council.
Attacking the NDA government, Issac said that with most states approving the GST constitutional amendment bill, "BJP has betrayed its true character".
Isaac said seven days prior notice has to be given for the meeting, but in an emergency, two days notice was enough.
However it was not possible to depute anybody to attend the meeting in place of the Finance Minister, he said.
"The Chairman (Union Minister) will decide the sitting position of each minister. The note also stated attendance has to be registered before the meeting", Issac said.
He said central government officers failed to note they are dealing with state ministers and not their subordinates.
Similarly, there was no dispute over chairmanship in the State Finance Ministers Empowered Committee for GST.
"But here the Vice-Chairman of the Council is being selected through election," he said.
The minister said the agenda note also gives in detail the procedure to be followed for voting and "there is not a single sentence of consensus in it."
Issac also said that this issue would be taken up by the state at the Council meeting.
The state assembly is slated to begin its sitting on September 26and is likely to take up the GST constitutional amendment bill.
On August 8, Parliament had passed the GST Constitution Bill, to replace different state and local taxes with a single unified value added tax system.
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